<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2015-03-24</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001374690</issuerCik>
        <issuerName>ZAFGEN, INC.</issuerName>
        <issuerTradingSymbol>ZFGN</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001346450</rptOwnerCik>
            <rptOwnerName>Atlas Venture Fund VII L P</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>25 FIRST STREET, SUITE 303</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02141</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001377726</rptOwnerCik>
            <rptOwnerName>Atlas Venture Associates VII, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>25 FIRST STREET, SUITE 303</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02141</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001377725</rptOwnerCik>
            <rptOwnerName>Atlas Venture Associates VII, Inc.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>25 FIRST STREET, SUITE 303</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02141</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2015-03-24</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>J</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>1000000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>4632730</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">On March 24, 2015, Atlas Venture Fund VII LP (&quot;Atlas Venture&quot;) distributed in-kind, without consideration, all 1,000,000 shares of the Issuer's Common Stock, pro-rata, to its limited partners.</footnote>
        <footnote id="F2">These shares were held directly by Atlas Venture. The general partner of Atlas Venture is Atlas Venture Associates VII, L.P. (&quot;AVA VII LP&quot;), and the general partner of AVA VII LP is Atlas Venture Associates VII, Inc. (&quot;AVA VII Inc.&quot;).  AVA VII LP and AVA VII Inc. disclaim beneficial ownership of such shares, except to the extent of a pecuniary interest, if any, therein.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>By: Atlas Venture Fund VII LP, By: Atlas Venture Associates VII, L.P., its general partner, By: Atlas Venture Associates VII, Inc., its general partner, /s/ Frank Castellucci, Secretary</signatureName>
        <signatureDate>2015-03-26</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>By:  Atlas Venture Associates VII, L.P., By: Atlas Venture Associates VII, Inc., its general partner, /s/ Frank Castellucci, Secretary</signatureName>
        <signatureDate>2015-03-26</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>By:  Atlas Venture Associates VII, Inc., /s/ Frank Castellucci, Secretary</signatureName>
        <signatureDate>2015-03-26</signatureDate>
    </ownerSignature>
</ownershipDocument>
