<?xml version="1.0" encoding="us-ascii"?>
<!-- DFS ActiveDisclosure(SM) XBRL Linkbase Document - http://www.dfsco.com/financial-services/ -->
<!-- Creation Date      : 2018-11-07T21:17:45.0961288+00:00 -->
<!-- Version            : 3.1.6852.22116 -->
<!-- Package ID         : f61bdb41bbda4ac8b413138d192abb51 -->
<!-- Copyright (c) 2018 Donnelley Financial, LLC. All Rights Reserved. -->
<linkbase xmlns="http://www.xbrl.org/2003/linkbase" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xbrldt="http://xbrl.org/2005/xbrldt" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
  <arcroleRef xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#all" arcroleURI="http://xbrl.org/int/dim/arcrole/all" />
  <arcroleRef xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#dimension-default" arcroleURI="http://xbrl.org/int/dim/arcrole/dimension-default" />
  <arcroleRef xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#dimension-domain" arcroleURI="http://xbrl.org/int/dim/arcrole/dimension-domain" />
  <arcroleRef xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#domain-member" arcroleURI="http://xbrl.org/int/dim/arcrole/domain-member" />
  <arcroleRef xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#hypercube-dimension" arcroleURI="http://xbrl.org/int/dim/arcrole/hypercube-dimension" />
  <roleRef xlink:type="simple" xlink:href="zfgn-20180930.xsd#TemplateLink" roleURI="http://www.zafgen.com/20180930/role/TemplateLink" />
  <roleRef roleURI="http://www.zafgen.com/20180930/taxonomy/role/DisclosureNatureOfBusinessAndBasisOfPresentationAdditionalInformationDetail" xlink:href="zfgn-20180930.xsd#Role_DisclosureNatureOfBusinessAndBasisOfPresentationAdditionalInformationDetail" xlink:type="simple" />
  <definitionLink xlink:type="extended" xlink:role="http://www.zafgen.com/20180930/taxonomy/role/DisclosureNatureOfBusinessAndBasisOfPresentationAdditionalInformationDetail">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CashCashEquivalentsAndShortTermInvestments" xlink:type="locator" xlink:label="us-gaap_CashCashEquivalentsAndShortTermInvestments" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RestrictedCashAndInvestments" xlink:type="locator" xlink:label="us-gaap_RestrictedCashAndInvestments" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DebtInstrumentFaceAmount" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentFaceAmount" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ProceedsFromIssuanceInitialPublicOffering" xlink:type="locator" xlink:label="us-gaap_ProceedsFromIssuanceInitialPublicOffering" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_SharesIssuedPricePerShare" xlink:type="locator" xlink:label="us-gaap_SharesIssuedPricePerShare" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StockIssuedDuringPeriodSharesNewIssues" xlink:type="locator" xlink:label="us-gaap_StockIssuedDuringPeriodSharesNewIssues" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_NetProceedsFromSaleOfSecurities" xlink:type="locator" xlink:label="zfgn_NetProceedsFromSaleOfSecurities" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RetainedEarningsAccumulatedDeficit" xlink:type="locator" xlink:label="us-gaap_RetainedEarningsAccumulatedDeficit" />
    <loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_EntityIncorporationDateOfIncorporation" xlink:type="locator" xlink:label="dei_EntityIncorporationDateOfIncorporation" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_TermLoanMember" xlink:type="locator" xlink:label="zfgn_TermLoanMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LongtermDebtTypeDomain" xlink:type="locator" xlink:label="us-gaap_LongtermDebtTypeDomain" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LongtermDebtTypeDomain" xlink:type="locator" xlink:label="us-gaap_LongtermDebtTypeDomain_2" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LongtermDebtTypeAxis" xlink:type="locator" xlink:label="us-gaap_LongtermDebtTypeAxis" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_IPOMember" xlink:type="locator" xlink:label="us-gaap_IPOMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_SaleOfStockNameOfTransactionDomain" xlink:type="locator" xlink:label="us-gaap_SaleOfStockNameOfTransactionDomain" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_SaleOfStockNameOfTransactionDomain" xlink:type="locator" xlink:label="us-gaap_SaleOfStockNameOfTransactionDomain_2" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_SubsidiarySaleOfStockAxis" xlink:type="locator" xlink:label="us-gaap_SubsidiarySaleOfStockAxis" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTable" xlink:type="locator" xlink:label="zfgn_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTable" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureLineItems" xlink:type="locator" xlink:label="zfgn_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureLineItems" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="zfgn_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureLineItems" xlink:to="zfgn_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTable" order="10010.00" priority="2" use="optional" xbrldt:contextElement="segment" xbrldt:closed="true" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="zfgn_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTable" xlink:to="us-gaap_SubsidiarySaleOfStockAxis" order="10040.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_SubsidiarySaleOfStockAxis" xlink:to="us-gaap_SaleOfStockNameOfTransactionDomain_2" order="10050.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_SubsidiarySaleOfStockAxis" xlink:to="us-gaap_SaleOfStockNameOfTransactionDomain" order="10070.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_SaleOfStockNameOfTransactionDomain" xlink:to="us-gaap_IPOMember" order="10090.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="zfgn_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTable" xlink:to="us-gaap_LongtermDebtTypeAxis" order="10140.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_LongtermDebtTypeAxis" xlink:to="us-gaap_LongtermDebtTypeDomain_2" order="10150.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_LongtermDebtTypeAxis" xlink:to="us-gaap_LongtermDebtTypeDomain" order="10170.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LongtermDebtTypeDomain" xlink:to="zfgn_TermLoanMember" order="10190.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="zfgn_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureLineItems" xlink:to="dei_EntityIncorporationDateOfIncorporation" order="10240.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="zfgn_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureLineItems" xlink:to="us-gaap_RetainedEarningsAccumulatedDeficit" order="10290.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="zfgn_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureLineItems" xlink:to="zfgn_NetProceedsFromSaleOfSecurities" order="10350.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="zfgn_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesNewIssues" order="10410.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="zfgn_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureLineItems" xlink:to="us-gaap_SharesIssuedPricePerShare" order="10470.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="zfgn_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureLineItems" xlink:to="us-gaap_ProceedsFromIssuanceInitialPublicOffering" order="10530.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="zfgn_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureLineItems" xlink:to="us-gaap_DebtInstrumentFaceAmount" order="10590.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="zfgn_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureLineItems" xlink:to="us-gaap_RestrictedCashAndInvestments" order="10650.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="zfgn_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureLineItems" xlink:to="us-gaap_CashCashEquivalentsAndShortTermInvestments" order="10740.00" priority="2" use="optional" />
  </definitionLink>
  <roleRef roleURI="http://www.zafgen.com/20180930/taxonomy/role/DisclosureSummaryOfSignificantAccountingPoliciesSummaryOfCommonStockEquivalentsOutstandingDetail" xlink:href="zfgn-20180930.xsd#Role_DisclosureSummaryOfSignificantAccountingPoliciesSummaryOfCommonStockEquivalentsOutstandingDetail" xlink:type="simple" />
  <definitionLink xlink:type="extended" xlink:role="http://www.zafgen.com/20180930/taxonomy/role/DisclosureSummaryOfSignificantAccountingPoliciesSummaryOfCommonStockEquivalentsOutstandingDetail">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount" xlink:type="locator" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RestrictedStockMember" xlink:type="locator" xlink:label="us-gaap_RestrictedStockMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EmployeeStockOptionMember" xlink:type="locator" xlink:label="us-gaap_EmployeeStockOptionMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AntidilutiveSecuritiesNameDomain" xlink:type="locator" xlink:label="us-gaap_AntidilutiveSecuritiesNameDomain" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AntidilutiveSecuritiesNameDomain" xlink:type="locator" xlink:label="us-gaap_AntidilutiveSecuritiesNameDomain_2" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:type="locator" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" xlink:type="locator" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" xlink:to="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" order="10010.00" priority="2" use="optional" xbrldt:contextElement="segment" xbrldt:closed="true" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" xlink:to="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" order="10040.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:to="us-gaap_AntidilutiveSecuritiesNameDomain_2" order="10050.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:to="us-gaap_AntidilutiveSecuritiesNameDomain" order="10070.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AntidilutiveSecuritiesNameDomain" xlink:to="us-gaap_EmployeeStockOptionMember" order="10090.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AntidilutiveSecuritiesNameDomain" xlink:to="us-gaap_RestrictedStockMember" order="10110.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" xlink:to="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount" order="10140.00" priority="2" use="optional" />
  </definitionLink>
  <roleRef roleURI="http://www.zafgen.com/20180930/taxonomy/role/DisclosureFairValueMeasurementsAndMarketableSecuritiesSummaryOfCashEquivalentsAndMarketableSecuritiesDetail" xlink:href="zfgn-20180930.xsd#Role_DisclosureFairValueMeasurementsAndMarketableSecuritiesSummaryOfCashEquivalentsAndMarketableSecuritiesDetail" xlink:type="simple" />
  <definitionLink xlink:type="extended" xlink:role="http://www.zafgen.com/20180930/taxonomy/role/DisclosureFairValueMeasurementsAndMarketableSecuritiesSummaryOfCashEquivalentsAndMarketableSecuritiesDetail">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AssetsFairValueDisclosure" xlink:type="locator" xlink:label="us-gaap_AssetsFairValueDisclosure" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecuritiesCurrent" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecuritiesCurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CashAndCashEquivalentsFairValueDisclosure" xlink:type="locator" xlink:label="us-gaap_CashAndCashEquivalentsFairValueDisclosure" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CertificatesOfDepositMember" xlink:type="locator" xlink:label="us-gaap_CertificatesOfDepositMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_USGovernmentCorporationsAndAgenciesSecuritiesMember" xlink:type="locator" xlink:label="us-gaap_USGovernmentCorporationsAndAgenciesSecuritiesMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CorporateBondSecuritiesMember" xlink:type="locator" xlink:label="us-gaap_CorporateBondSecuritiesMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommercialPaperMember" xlink:type="locator" xlink:label="us-gaap_CommercialPaperMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_MoneyMarketFundsMember" xlink:type="locator" xlink:label="us-gaap_MoneyMarketFundsMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_InvestmentTypeCategorizationMember" xlink:type="locator" xlink:label="us-gaap_InvestmentTypeCategorizationMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_InvestmentTypeCategorizationMember" xlink:type="locator" xlink:label="us-gaap_InvestmentTypeCategorizationMember_2" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_InvestmentTypeAxis" xlink:type="locator" xlink:label="us-gaap_InvestmentTypeAxis" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FairValueInputsLevel3Member" xlink:type="locator" xlink:label="us-gaap_FairValueInputsLevel3Member" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FairValueInputsLevel2Member" xlink:type="locator" xlink:label="us-gaap_FairValueInputsLevel2Member" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FairValueInputsLevel1Member" xlink:type="locator" xlink:label="us-gaap_FairValueInputsLevel1Member" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:type="locator" xlink:label="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:type="locator" xlink:label="us-gaap_FairValueMeasurementsFairValueHierarchyDomain_2" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:type="locator" xlink:label="us-gaap_FairValueByFairValueHierarchyLevelAxis" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:type="locator" xlink:label="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:type="locator" xlink:label="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:to="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" order="10030.00" priority="2" use="optional" xbrldt:contextElement="segment" xbrldt:closed="true" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:to="us-gaap_FairValueByFairValueHierarchyLevelAxis" order="10060.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:to="us-gaap_FairValueMeasurementsFairValueHierarchyDomain_2" order="10070.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:to="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" order="10090.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:to="us-gaap_FairValueInputsLevel1Member" order="10110.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:to="us-gaap_FairValueInputsLevel2Member" order="10130.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:to="us-gaap_FairValueInputsLevel3Member" order="10150.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:to="us-gaap_InvestmentTypeAxis" order="10160.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_InvestmentTypeAxis" xlink:to="us-gaap_InvestmentTypeCategorizationMember_2" order="10170.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_InvestmentTypeAxis" xlink:to="us-gaap_InvestmentTypeCategorizationMember" order="10190.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_InvestmentTypeCategorizationMember" xlink:to="us-gaap_MoneyMarketFundsMember" order="10210.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_InvestmentTypeCategorizationMember" xlink:to="us-gaap_CommercialPaperMember" order="10230.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_InvestmentTypeCategorizationMember" xlink:to="us-gaap_CorporateBondSecuritiesMember" order="10250.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_InvestmentTypeCategorizationMember" xlink:to="us-gaap_USGovernmentCorporationsAndAgenciesSecuritiesMember" order="10310.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_InvestmentTypeCategorizationMember" xlink:to="us-gaap_CertificatesOfDepositMember" order="10570.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:to="us-gaap_CashAndCashEquivalentsFairValueDisclosure" order="10600.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:to="us-gaap_AvailableForSaleSecuritiesDebtSecuritiesCurrent" order="10920.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:to="us-gaap_AssetsFairValueDisclosure" order="11240.00" priority="2" use="optional" />
  </definitionLink>
  <roleRef roleURI="http://www.zafgen.com/20180930/taxonomy/role/DisclosureFairValueMeasurementsAndMarketableSecuritiesSummaryOfMarketableSecuritiesDetail" xlink:href="zfgn-20180930.xsd#Role_DisclosureFairValueMeasurementsAndMarketableSecuritiesSummaryOfMarketableSecuritiesDetail" xlink:type="simple" />
  <definitionLink xlink:type="extended" xlink:role="http://www.zafgen.com/20180930/taxonomy/role/DisclosureFairValueMeasurementsAndMarketableSecuritiesSummaryOfMarketableSecuritiesDetail">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecuritiesCurrent" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecuritiesCurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CertificatesOfDepositMember" xlink:type="locator" xlink:label="us-gaap_CertificatesOfDepositMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_USGovernmentCorporationsAndAgenciesSecuritiesMember" xlink:type="locator" xlink:label="us-gaap_USGovernmentCorporationsAndAgenciesSecuritiesMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommercialPaperMember" xlink:type="locator" xlink:label="us-gaap_CommercialPaperMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CorporateBondSecuritiesMember" xlink:type="locator" xlink:label="us-gaap_CorporateBondSecuritiesMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_InvestmentTypeCategorizationMember" xlink:type="locator" xlink:label="us-gaap_InvestmentTypeCategorizationMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_InvestmentTypeAxis" xlink:type="locator" xlink:label="us-gaap_InvestmentTypeAxis" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DebtSecuritiesAvailableForSaleTable" xlink:type="locator" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleTable" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:type="locator" xlink:label="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_DebtSecuritiesAvailableForSaleTable" order="10040.00" priority="2" use="optional" xbrldt:contextElement="segment" xbrldt:closed="true" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_DebtSecuritiesAvailableForSaleTable" xlink:to="us-gaap_InvestmentTypeAxis" order="10070.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_InvestmentTypeAxis" xlink:to="us-gaap_InvestmentTypeCategorizationMember" order="10100.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_InvestmentTypeCategorizationMember" xlink:to="us-gaap_CorporateBondSecuritiesMember" order="10120.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_InvestmentTypeCategorizationMember" xlink:to="us-gaap_CommercialPaperMember" order="10140.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_InvestmentTypeCategorizationMember" xlink:to="us-gaap_USGovernmentCorporationsAndAgenciesSecuritiesMember" order="10160.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_InvestmentTypeCategorizationMember" xlink:to="us-gaap_CertificatesOfDepositMember" order="10260.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis" order="10290.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" order="10490.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" order="10690.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_AvailableForSaleSecuritiesDebtSecuritiesCurrent" order="10890.00" priority="2" use="optional" />
  </definitionLink>
  <roleRef roleURI="http://www.zafgen.com/20180930/taxonomy/role/DisclosureNotesPayableAdditionalInformationDetail" xlink:href="zfgn-20180930.xsd#Role_DisclosureNotesPayableAdditionalInformationDetail" xlink:type="simple" />
  <definitionLink xlink:type="extended" xlink:role="http://www.zafgen.com/20180930/taxonomy/role/DisclosureNotesPayableAdditionalInformationDetail">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LineOfCreditFacilityPeriodicPaymentInterest" xlink:type="locator" xlink:label="us-gaap_LineOfCreditFacilityPeriodicPaymentInterest" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DebtInstrumentInterestRateDuringPeriod" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentInterestRateDuringPeriod" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DebtInstrumentPeriodicPaymentInterest" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentPeriodicPaymentInterest" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_InterestPayableCurrentAndNoncurrent" xlink:type="locator" xlink:label="us-gaap_InterestPayableCurrentAndNoncurrent" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LongTermDebt" xlink:type="locator" xlink:label="us-gaap_LongTermDebt" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_NotesPayable" xlink:type="locator" xlink:label="us-gaap_NotesPayable" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_LineOfCreditFacilityDebtDefaultMinimumAmount" xlink:type="locator" xlink:label="zfgn_LineOfCreditFacilityDebtDefaultMinimumAmount" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_DebtInstrumentRestrictiveCovenantsInvestmentInSubsidiaries" xlink:type="locator" xlink:label="zfgn_DebtInstrumentRestrictiveCovenantsInvestmentInSubsidiaries" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_PercentageOfPrincipalBalanceToBeSecuredInRestrictedCashAccount" xlink:type="locator" xlink:label="zfgn_PercentageOfPrincipalBalanceToBeSecuredInRestrictedCashAccount" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_CashCashEquivalentsAndShortTermInvestmentsPercentage" xlink:type="locator" xlink:label="zfgn_CashCashEquivalentsAndShortTermInvestmentsPercentage" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CashCashEquivalentsAndShortTermInvestments" xlink:type="locator" xlink:label="us-gaap_CashCashEquivalentsAndShortTermInvestments" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DebtInstrumentCovenantDescription" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentCovenantDescription" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RestrictedCashAndInvestments" xlink:type="locator" xlink:label="us-gaap_RestrictedCashAndInvestments" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_RestrictedCashAndInvestmentsAsPercentageOfOutstandingPrincipalAmount" xlink:type="locator" xlink:label="zfgn_RestrictedCashAndInvestmentsAsPercentageOfOutstandingPrincipalAmount" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DebtInstrumentIncreaseAccruedInterest" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentIncreaseAccruedInterest" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_DebtInstrumentFeePercentage" xlink:type="locator" xlink:label="zfgn_DebtInstrumentFeePercentage" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DebtInstrumentInterestRateEffectivePercentage" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentInterestRateEffectivePercentage" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DebtInstrumentBasisSpreadOnVariableRate1" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentBasisSpreadOnVariableRate1" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DebtInstrumentDescriptionOfVariableRateBasis" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentDescriptionOfVariableRateBasis" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DebtInstrumentMaturityDate" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentMaturityDate" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DebtInstrumentDescription" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentDescription" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ProceedsFromNotesPayable" xlink:type="locator" xlink:label="us-gaap_ProceedsFromNotesPayable" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DebtInstrumentFaceAmount" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentFaceAmount" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_SecuredDebtMember" xlink:type="locator" xlink:label="us-gaap_SecuredDebtMember" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_TwoThousandAndFourteenCreditFacilityMember" xlink:type="locator" xlink:label="zfgn_TwoThousandAndFourteenCreditFacilityMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CreditFacilityDomain" xlink:type="locator" xlink:label="us-gaap_CreditFacilityDomain" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CreditFacilityDomain" xlink:type="locator" xlink:label="us-gaap_CreditFacilityDomain_2" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CreditFacilityAxis" xlink:type="locator" xlink:label="us-gaap_CreditFacilityAxis" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_MaximumMember" xlink:type="locator" xlink:label="srt_MaximumMember" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_MinimumMember" xlink:type="locator" xlink:label="srt_MinimumMember" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_RangeMember" xlink:type="locator" xlink:label="srt_RangeMember" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_RangeMember" xlink:type="locator" xlink:label="srt_RangeMember_2" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_RangeAxis" xlink:type="locator" xlink:label="srt_RangeAxis" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_TermLoanMember" xlink:type="locator" xlink:label="zfgn_TermLoanMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LongtermDebtTypeDomain" xlink:type="locator" xlink:label="us-gaap_LongtermDebtTypeDomain" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LongtermDebtTypeAxis" xlink:type="locator" xlink:label="us-gaap_LongtermDebtTypeAxis" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DebtInstrumentTable" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentTable" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DebtInstrumentLineItems" xlink:type="locator" xlink:label="us-gaap_DebtInstrumentLineItems" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentTable" order="10010.00" priority="2" use="optional" xbrldt:contextElement="segment" xbrldt:closed="true" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="us-gaap_LongtermDebtTypeAxis" order="10040.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_LongtermDebtTypeAxis" xlink:to="us-gaap_LongtermDebtTypeDomain" order="10070.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LongtermDebtTypeDomain" xlink:to="zfgn_TermLoanMember" order="10090.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="srt_RangeAxis" order="10360.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember_2" order="10370.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" order="10390.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MinimumMember" order="10410.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MaximumMember" order="10430.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="us-gaap_CreditFacilityAxis" order="10820.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_CreditFacilityAxis" xlink:to="us-gaap_CreditFacilityDomain_2" order="10830.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_CreditFacilityAxis" xlink:to="us-gaap_CreditFacilityDomain" order="10850.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CreditFacilityDomain" xlink:to="zfgn_TwoThousandAndFourteenCreditFacilityMember" order="10870.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LongtermDebtTypeDomain" xlink:to="us-gaap_SecuredDebtMember" order="10950.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentFaceAmount" order="11000.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_ProceedsFromNotesPayable" order="11020.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentDescription" order="11070.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentMaturityDate" order="11110.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentDescriptionOfVariableRateBasis" order="11150.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentBasisSpreadOnVariableRate1" order="11190.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentInterestRateEffectivePercentage" order="11230.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="zfgn_DebtInstrumentFeePercentage" order="11270.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentIncreaseAccruedInterest" order="11310.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="zfgn_RestrictedCashAndInvestmentsAsPercentageOfOutstandingPrincipalAmount" order="11380.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_RestrictedCashAndInvestments" order="11420.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentCovenantDescription" order="11490.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_CashCashEquivalentsAndShortTermInvestments" order="11510.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="zfgn_CashCashEquivalentsAndShortTermInvestmentsPercentage" order="11530.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="zfgn_PercentageOfPrincipalBalanceToBeSecuredInRestrictedCashAccount" order="11550.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="zfgn_DebtInstrumentRestrictiveCovenantsInvestmentInSubsidiaries" order="11600.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="zfgn_LineOfCreditFacilityDebtDefaultMinimumAmount" order="11650.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_NotesPayable" order="11700.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_LongTermDebt" order="11740.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_InterestPayableCurrentAndNoncurrent" order="11780.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentPeriodicPaymentInterest" order="11850.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentInterestRateDuringPeriod" order="11890.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_LineOfCreditFacilityPeriodicPaymentInterest" order="11960.00" priority="2" use="optional" />
  </definitionLink>
  <roleRef roleURI="http://www.zafgen.com/20180930/taxonomy/role/DisclosureStockBasedAwardsAdditionalInformationDetail" xlink:href="zfgn-20180930.xsd#Role_DisclosureStockBasedAwardsAdditionalInformationDetail" xlink:type="simple" />
  <definitionLink xlink:type="extended" xlink:role="http://www.zafgen.com/20180930/taxonomy/role/DisclosureStockBasedAwardsAdditionalInformationDetail">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOtherIncreasesDecreasesInPeriod" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOtherIncreasesDecreasesInPeriod" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrant" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrant" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_TwoThousandAndFourteenEmployeeStockPurchasePlanMember" xlink:type="locator" xlink:label="zfgn_TwoThousandAndFourteenEmployeeStockPurchasePlanMember" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_TwoThousandFourteenStockOptionMember" xlink:type="locator" xlink:label="zfgn_TwoThousandFourteenStockOptionMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PlanNameDomain" xlink:type="locator" xlink:label="us-gaap_PlanNameDomain" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PlanNameDomain" xlink:type="locator" xlink:label="us-gaap_PlanNameDomain_2" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PlanNameAxis" xlink:type="locator" xlink:label="us-gaap_PlanNameAxis" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" order="10010.00" priority="2" use="optional" xbrldt:contextElement="segment" xbrldt:closed="true" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_PlanNameAxis" order="10040.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_PlanNameAxis" xlink:to="us-gaap_PlanNameDomain_2" order="10050.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_PlanNameAxis" xlink:to="us-gaap_PlanNameDomain" order="10070.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PlanNameDomain" xlink:to="zfgn_TwoThousandFourteenStockOptionMember" order="10090.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PlanNameDomain" xlink:to="zfgn_TwoThousandAndFourteenEmployeeStockPurchasePlanMember" order="10130.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrant" order="10160.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOtherIncreasesDecreasesInPeriod" order="10180.00" priority="2" use="optional" />
  </definitionLink>
  <roleRef roleURI="http://www.zafgen.com/20180930/taxonomy/role/DisclosureStockBasedAwardsSummaryOfStockBasedCompensationExpenseRelatedToStockOptionsRestrictedCommonStockAndESPPDetail" xlink:href="zfgn-20180930.xsd#Role_DisclosureStockBasedAwardsSummaryOfStockBasedCompensationExpenseRelatedToStockOptionsRestrictedCommonStockAndESPPDetail" xlink:type="simple" />
  <definitionLink xlink:type="extended" xlink:role="http://www.zafgen.com/20180930/taxonomy/role/DisclosureStockBasedAwardsSummaryOfStockBasedCompensationExpenseRelatedToStockOptionsRestrictedCommonStockAndESPPDetail">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AllocatedShareBasedCompensationExpense" xlink:type="locator" xlink:label="us-gaap_AllocatedShareBasedCompensationExpense" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_GeneralAndAdministrativeExpenseMember" xlink:type="locator" xlink:label="us-gaap_GeneralAndAdministrativeExpenseMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ResearchAndDevelopmentExpenseMember" xlink:type="locator" xlink:label="us-gaap_ResearchAndDevelopmentExpenseMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_IncomeStatementLocationDomain" xlink:type="locator" xlink:label="us-gaap_IncomeStatementLocationDomain" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_IncomeStatementLocationDomain" xlink:type="locator" xlink:label="us-gaap_IncomeStatementLocationDomain_2" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_IncomeStatementLocationAxis" xlink:type="locator" xlink:label="us-gaap_IncomeStatementLocationAxis" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" order="10010.00" priority="2" use="optional" xbrldt:contextElement="segment" xbrldt:closed="true" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_IncomeStatementLocationAxis" order="10040.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_IncomeStatementLocationAxis" xlink:to="us-gaap_IncomeStatementLocationDomain_2" order="10050.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_IncomeStatementLocationAxis" xlink:to="us-gaap_IncomeStatementLocationDomain" order="10070.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_IncomeStatementLocationDomain" xlink:to="us-gaap_ResearchAndDevelopmentExpenseMember" order="10090.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_IncomeStatementLocationDomain" xlink:to="us-gaap_GeneralAndAdministrativeExpenseMember" order="10110.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_AllocatedShareBasedCompensationExpense" order="10140.00" priority="2" use="optional" />
  </definitionLink>
  <roleRef roleURI="http://www.zafgen.com/20180930/taxonomy/role/DisclosureCommitmentsAndContingenciesAdditionalInformationDetail" xlink:href="zfgn-20180930.xsd#Role_DisclosureCommitmentsAndContingenciesAdditionalInformationDetail" xlink:type="simple" />
  <definitionLink xlink:type="extended" xlink:role="http://www.zafgen.com/20180930/taxonomy/role/DisclosureCommitmentsAndContingenciesAdditionalInformationDetail">
    <loc xlink:href="zfgn-20180930.xsd#zfgn_MilestoneLiability" xlink:type="locator" xlink:label="zfgn_MilestoneLiability" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_LicensingFeesPerProductMaximum" xlink:type="locator" xlink:label="zfgn_LicensingFeesPerProductMaximum" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_MilestonePaymentAmount" xlink:type="locator" xlink:label="zfgn_MilestonePaymentAmount" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeasesRentExpenseNet" xlink:type="locator" xlink:label="us-gaap_OperatingLeasesRentExpenseNet" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeasesRentExpenseSubleaseRentals1" xlink:type="locator" xlink:label="us-gaap_OperatingLeasesRentExpenseSubleaseRentals1" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_SubleaseExpirationDate" xlink:type="locator" xlink:label="zfgn_SubleaseExpirationDate" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_SubleaseAreaOfRealEstateProperty" xlink:type="locator" xlink:label="zfgn_SubleaseAreaOfRealEstateProperty" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_OperatingLeasesNumberOfOptionsToExtendLease" xlink:type="locator" xlink:label="zfgn_OperatingLeasesNumberOfOptionsToExtendLease" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LesseeOperatingLeaseRenewalTerm" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseRenewalTerm" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LeaseExpirationDate1" xlink:type="locator" xlink:label="us-gaap_LeaseExpirationDate1" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_DevelopmentBasedMilestonesMember" xlink:type="locator" xlink:label="zfgn_DevelopmentBasedMilestonesMember" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_SubsequentLicensedProductMember" xlink:type="locator" xlink:label="zfgn_SubsequentLicensedProductMember" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_ProductCommercializationMilestonesMember" xlink:type="locator" xlink:label="zfgn_ProductCommercializationMilestonesMember" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_PreCommercializationMilestonesMember" xlink:type="locator" xlink:label="zfgn_PreCommercializationMilestonesMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LongTermPurchaseCommitmentCategoryOfItemPurchasedDomain" xlink:type="locator" xlink:label="us-gaap_LongTermPurchaseCommitmentCategoryOfItemPurchasedDomain" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LongTermPurchaseCommitmentCategoryOfItemPurchasedDomain" xlink:type="locator" xlink:label="us-gaap_LongTermPurchaseCommitmentCategoryOfItemPurchasedDomain_2" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LongTermPurchaseCommitmentByCategoryOfItemPurchasedAxis" xlink:type="locator" xlink:label="us-gaap_LongTermPurchaseCommitmentByCategoryOfItemPurchasedAxis" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_MinimumMember" xlink:type="locator" xlink:label="srt_MinimumMember" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_MaximumMember" xlink:type="locator" xlink:label="srt_MaximumMember" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_RangeMember" xlink:type="locator" xlink:label="srt_RangeMember" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_RangeAxis" xlink:type="locator" xlink:label="srt_RangeAxis" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScenarioForecastMember" xlink:type="locator" xlink:label="us-gaap_ScenarioForecastMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScenarioUnspecifiedDomain" xlink:type="locator" xlink:label="us-gaap_ScenarioUnspecifiedDomain" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScenarioUnspecifiedDomain" xlink:type="locator" xlink:label="us-gaap_ScenarioUnspecifiedDomain_2" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StatementScenarioAxis" xlink:type="locator" xlink:label="us-gaap_StatementScenarioAxis" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_UnrelatedThirdPartyMember" xlink:type="locator" xlink:label="zfgn_UnrelatedThirdPartyMember" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_RepurchaseAgreementCounterpartyNameDomain" xlink:type="locator" xlink:label="srt_RepurchaseAgreementCounterpartyNameDomain" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_RepurchaseAgreementCounterpartyNameDomain" xlink:type="locator" xlink:label="srt_RepurchaseAgreementCounterpartyNameDomain_2" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_CounterpartyNameAxis" xlink:type="locator" xlink:label="srt_CounterpartyNameAxis" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_AdditionalOfficeSpaceTwoMember" xlink:type="locator" xlink:label="zfgn_AdditionalOfficeSpaceTwoMember" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_AdditionalOfficeSpaceMember" xlink:type="locator" xlink:label="zfgn_AdditionalOfficeSpaceMember" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_OfficeSpaceLeaseMember" xlink:type="locator" xlink:label="zfgn_OfficeSpaceLeaseMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LeaseArrangementTypeDomain" xlink:type="locator" xlink:label="us-gaap_LeaseArrangementTypeDomain" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LeaseArrangementTypeDomain" xlink:type="locator" xlink:label="us-gaap_LeaseArrangementTypeDomain_2" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LeaseArrangementTypeAxis" xlink:type="locator" xlink:label="us-gaap_LeaseArrangementTypeAxis" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OtherCommitmentsTable" xlink:type="locator" xlink:label="us-gaap_OtherCommitmentsTable" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OtherCommitmentsLineItems" xlink:type="locator" xlink:label="us-gaap_OtherCommitmentsLineItems" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_OtherCommitmentsLineItems" xlink:to="us-gaap_OtherCommitmentsTable" order="10010.00" priority="2" use="optional" xbrldt:contextElement="segment" xbrldt:closed="true" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_OtherCommitmentsTable" xlink:to="us-gaap_LeaseArrangementTypeAxis" order="10040.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_LeaseArrangementTypeAxis" xlink:to="us-gaap_LeaseArrangementTypeDomain_2" order="10050.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_LeaseArrangementTypeAxis" xlink:to="us-gaap_LeaseArrangementTypeDomain" order="10070.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LeaseArrangementTypeDomain" xlink:to="zfgn_OfficeSpaceLeaseMember" order="10090.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LeaseArrangementTypeDomain" xlink:to="zfgn_AdditionalOfficeSpaceMember" order="10130.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LeaseArrangementTypeDomain" xlink:to="zfgn_AdditionalOfficeSpaceTwoMember" order="10270.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_OtherCommitmentsTable" xlink:to="srt_CounterpartyNameAxis" order="10300.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="srt_CounterpartyNameAxis" xlink:to="srt_RepurchaseAgreementCounterpartyNameDomain_2" order="10310.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_CounterpartyNameAxis" xlink:to="srt_RepurchaseAgreementCounterpartyNameDomain" order="10330.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RepurchaseAgreementCounterpartyNameDomain" xlink:to="zfgn_UnrelatedThirdPartyMember" order="10350.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_OtherCommitmentsTable" xlink:to="us-gaap_StatementScenarioAxis" order="10400.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_StatementScenarioAxis" xlink:to="us-gaap_ScenarioUnspecifiedDomain_2" order="10410.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_StatementScenarioAxis" xlink:to="us-gaap_ScenarioUnspecifiedDomain" order="10430.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ScenarioUnspecifiedDomain" xlink:to="us-gaap_ScenarioForecastMember" order="10450.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_OtherCommitmentsTable" xlink:to="srt_RangeAxis" order="10460.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" order="10490.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MaximumMember" order="10510.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MinimumMember" order="10550.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_OtherCommitmentsTable" xlink:to="us-gaap_LongTermPurchaseCommitmentByCategoryOfItemPurchasedAxis" order="10560.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_LongTermPurchaseCommitmentByCategoryOfItemPurchasedAxis" xlink:to="us-gaap_LongTermPurchaseCommitmentCategoryOfItemPurchasedDomain_2" order="10570.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_LongTermPurchaseCommitmentByCategoryOfItemPurchasedAxis" xlink:to="us-gaap_LongTermPurchaseCommitmentCategoryOfItemPurchasedDomain" order="10590.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LongTermPurchaseCommitmentCategoryOfItemPurchasedDomain" xlink:to="zfgn_PreCommercializationMilestonesMember" order="10610.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LongTermPurchaseCommitmentCategoryOfItemPurchasedDomain" xlink:to="zfgn_ProductCommercializationMilestonesMember" order="10630.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LongTermPurchaseCommitmentCategoryOfItemPurchasedDomain" xlink:to="zfgn_SubsequentLicensedProductMember" order="10650.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LongTermPurchaseCommitmentCategoryOfItemPurchasedDomain" xlink:to="zfgn_DevelopmentBasedMilestonesMember" order="10710.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OtherCommitmentsLineItems" xlink:to="us-gaap_LeaseExpirationDate1" order="10740.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OtherCommitmentsLineItems" xlink:to="us-gaap_LesseeOperatingLeaseRenewalTerm" order="10900.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OtherCommitmentsLineItems" xlink:to="zfgn_OperatingLeasesNumberOfOptionsToExtendLease" order="10940.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OtherCommitmentsLineItems" xlink:to="zfgn_SubleaseAreaOfRealEstateProperty" order="10980.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OtherCommitmentsLineItems" xlink:to="zfgn_SubleaseExpirationDate" order="11020.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OtherCommitmentsLineItems" xlink:to="us-gaap_OperatingLeasesRentExpenseSubleaseRentals1" order="11060.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OtherCommitmentsLineItems" xlink:to="us-gaap_OperatingLeasesRentExpenseNet" order="11210.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OtherCommitmentsLineItems" xlink:to="zfgn_MilestonePaymentAmount" order="11320.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OtherCommitmentsLineItems" xlink:to="zfgn_LicensingFeesPerProductMaximum" order="11360.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OtherCommitmentsLineItems" xlink:to="zfgn_MilestoneLiability" order="11410.00" priority="2" use="optional" />
  </definitionLink>
  <roleRef roleURI="http://www.zafgen.com/20180930/taxonomy/role/DisclosureRetirementPlanAdditionalInformationDetail" xlink:href="zfgn-20180930.xsd#Role_DisclosureRetirementPlanAdditionalInformationDetail" xlink:type="simple" />
  <definitionLink xlink:type="extended" xlink:role="http://www.zafgen.com/20180930/taxonomy/role/DisclosureRetirementPlanAdditionalInformationDetail">
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DefinedContributionPlanCostRecognized" xlink:type="locator" xlink:label="us-gaap_DefinedContributionPlanCostRecognized" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DefinedContributionPlanEmployerMatchingContributionPercent" xlink:type="locator" xlink:label="us-gaap_DefinedContributionPlanEmployerMatchingContributionPercent" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_SIMPLEIRAPlanMember" xlink:type="locator" xlink:label="zfgn_SIMPLEIRAPlanMember" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_MinimumMember" xlink:type="locator" xlink:label="srt_MinimumMember" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_MaximumMember" xlink:type="locator" xlink:label="srt_MaximumMember" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_RangeMember" xlink:type="locator" xlink:label="srt_RangeMember" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_RangeAxis" xlink:type="locator" xlink:label="srt_RangeAxis" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_Retirement401KPlanMember" xlink:type="locator" xlink:label="zfgn_Retirement401KPlanMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RetirementPlanTypeDomain" xlink:type="locator" xlink:label="us-gaap_RetirementPlanTypeDomain" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RetirementPlanTypeDomain" xlink:type="locator" xlink:label="us-gaap_RetirementPlanTypeDomain_2" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RetirementPlanTypeAxis" xlink:type="locator" xlink:label="us-gaap_RetirementPlanTypeAxis" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DefinedContributionPlanTable" xlink:type="locator" xlink:label="us-gaap_DefinedContributionPlanTable" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DefinedContributionPlanDisclosureLineItems" xlink:type="locator" xlink:label="us-gaap_DefinedContributionPlanDisclosureLineItems" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_DefinedContributionPlanDisclosureLineItems" xlink:to="us-gaap_DefinedContributionPlanTable" order="10010.00" priority="2" use="optional" xbrldt:contextElement="segment" xbrldt:closed="true" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_DefinedContributionPlanTable" xlink:to="us-gaap_RetirementPlanTypeAxis" order="10040.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_RetirementPlanTypeAxis" xlink:to="us-gaap_RetirementPlanTypeDomain_2" order="10050.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_RetirementPlanTypeAxis" xlink:to="us-gaap_RetirementPlanTypeDomain" order="10070.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RetirementPlanTypeDomain" xlink:to="zfgn_Retirement401KPlanMember" order="10090.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_DefinedContributionPlanTable" xlink:to="srt_RangeAxis" order="10120.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" order="10150.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MaximumMember" order="10170.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MinimumMember" order="10190.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RetirementPlanTypeDomain" xlink:to="zfgn_SIMPLEIRAPlanMember" order="10250.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DefinedContributionPlanDisclosureLineItems" xlink:to="us-gaap_DefinedContributionPlanEmployerMatchingContributionPercent" order="10380.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DefinedContributionPlanDisclosureLineItems" xlink:to="us-gaap_DefinedContributionPlanCostRecognized" order="10430.00" priority="2" use="optional" />
  </definitionLink>
  <roleRef roleURI="http://www.zafgen.com/20180930/taxonomy/role/DisclosureAustraliaResearchAndDevelopmentTaxIncentiveAdditionalInformationDetail" xlink:href="zfgn-20180930.xsd#Role_DisclosureAustraliaResearchAndDevelopmentTaxIncentiveAdditionalInformationDetail" xlink:type="simple" />
  <definitionLink xlink:type="extended" xlink:role="http://www.zafgen.com/20180930/taxonomy/role/DisclosureAustraliaResearchAndDevelopmentTaxIncentiveAdditionalInformationDetail">
    <loc xlink:href="zfgn-20180930.xsd#zfgn_TaxIncentiveReceivable" xlink:type="locator" xlink:label="zfgn_TaxIncentiveReceivable" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ForeignCurrencyTransactionGainLossUnrealized" xlink:type="locator" xlink:label="us-gaap_ForeignCurrencyTransactionGainLossUnrealized" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_PercentageReductionResearchAndDevelopmentCosts" xlink:type="locator" xlink:label="zfgn_PercentageReductionResearchAndDevelopmentCosts" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_TaxIncentiveResearchAndDevelopmentActivities" xlink:type="locator" xlink:label="zfgn_TaxIncentiveResearchAndDevelopmentActivities" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_EffectiveTaxIncentiveRateRelatedToResearchAndDevelopment" xlink:type="locator" xlink:label="zfgn_EffectiveTaxIncentiveRateRelatedToResearchAndDevelopment" />
    <loc xlink:href="http://xbrl.sec.gov/country/2017/country-2017-01-31.xsd#country_AU" xlink:type="locator" xlink:label="country_AU" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_SegmentGeographicalDomain" xlink:type="locator" xlink:label="srt_SegmentGeographicalDomain" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_SegmentGeographicalDomain" xlink:type="locator" xlink:label="srt_SegmentGeographicalDomain_2" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_StatementGeographicalAxis" xlink:type="locator" xlink:label="srt_StatementGeographicalAxis" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_MinimumMember" xlink:type="locator" xlink:label="srt_MinimumMember" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_MaximumMember" xlink:type="locator" xlink:label="srt_MaximumMember" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_RangeMember" xlink:type="locator" xlink:label="srt_RangeMember" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_RangeAxis" xlink:type="locator" xlink:label="srt_RangeAxis" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_SubsidiariesMember" xlink:type="locator" xlink:label="srt_SubsidiariesMember" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_ConsolidatedEntitiesDomain" xlink:type="locator" xlink:label="srt_ConsolidatedEntitiesDomain" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_ConsolidatedEntitiesDomain" xlink:type="locator" xlink:label="srt_ConsolidatedEntitiesDomain_2" />
    <loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_ConsolidatedEntitiesAxis" xlink:type="locator" xlink:label="srt_ConsolidatedEntitiesAxis" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ResearchAndDevelopmentExpenseMember" xlink:type="locator" xlink:label="us-gaap_ResearchAndDevelopmentExpenseMember" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_IncomeStatementLocationDomain" xlink:type="locator" xlink:label="us-gaap_IncomeStatementLocationDomain" />
    <loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_IncomeStatementLocationAxis" xlink:type="locator" xlink:label="us-gaap_IncomeStatementLocationAxis" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_ResearchAndDevelopmentExpensesTable" xlink:type="locator" xlink:label="zfgn_ResearchAndDevelopmentExpensesTable" />
    <loc xlink:href="zfgn-20180930.xsd#zfgn_ResearchAndDevelopmentTaxIncentiveLineItems" xlink:type="locator" xlink:label="zfgn_ResearchAndDevelopmentTaxIncentiveLineItems" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="zfgn_ResearchAndDevelopmentTaxIncentiveLineItems" xlink:to="zfgn_ResearchAndDevelopmentExpensesTable" order="10010.00" priority="2" use="optional" xbrldt:contextElement="segment" xbrldt:closed="true" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="zfgn_ResearchAndDevelopmentExpensesTable" xlink:to="us-gaap_IncomeStatementLocationAxis" order="10040.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_IncomeStatementLocationAxis" xlink:to="us-gaap_IncomeStatementLocationDomain" order="10070.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_IncomeStatementLocationDomain" xlink:to="us-gaap_ResearchAndDevelopmentExpenseMember" order="10090.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="zfgn_ResearchAndDevelopmentExpensesTable" xlink:to="srt_ConsolidatedEntitiesAxis" order="10140.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="srt_ConsolidatedEntitiesAxis" xlink:to="srt_ConsolidatedEntitiesDomain_2" order="10150.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_ConsolidatedEntitiesAxis" xlink:to="srt_ConsolidatedEntitiesDomain" order="10170.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_ConsolidatedEntitiesDomain" xlink:to="srt_SubsidiariesMember" order="10190.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="zfgn_ResearchAndDevelopmentExpensesTable" xlink:to="srt_RangeAxis" order="10300.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" order="10330.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MaximumMember" order="10350.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MinimumMember" order="10370.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="zfgn_ResearchAndDevelopmentExpensesTable" xlink:to="srt_StatementGeographicalAxis" order="10380.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="srt_StatementGeographicalAxis" xlink:to="srt_SegmentGeographicalDomain_2" order="10390.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_StatementGeographicalAxis" xlink:to="srt_SegmentGeographicalDomain" order="10410.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_SegmentGeographicalDomain" xlink:to="country_AU" order="10430.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="zfgn_ResearchAndDevelopmentTaxIncentiveLineItems" xlink:to="zfgn_EffectiveTaxIncentiveRateRelatedToResearchAndDevelopment" order="10460.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="zfgn_ResearchAndDevelopmentTaxIncentiveLineItems" xlink:to="zfgn_TaxIncentiveResearchAndDevelopmentActivities" order="10540.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="zfgn_ResearchAndDevelopmentTaxIncentiveLineItems" xlink:to="zfgn_PercentageReductionResearchAndDevelopmentCosts" order="10620.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="zfgn_ResearchAndDevelopmentTaxIncentiveLineItems" xlink:to="us-gaap_ForeignCurrencyTransactionGainLossUnrealized" order="10700.00" priority="2" use="optional" />
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="zfgn_ResearchAndDevelopmentTaxIncentiveLineItems" xlink:to="zfgn_TaxIncentiveReceivable" order="10860.00" priority="2" use="optional" />
  </definitionLink>
</linkbase>
