<SEC-DOCUMENT>0000899243-16-012289.txt : 20160127
<SEC-HEADER>0000899243-16-012289.hdr.sgml : 20160127
<ACCEPTANCE-DATETIME>20160127211929
ACCESSION NUMBER:		0000899243-16-012289
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20160125
FILED AS OF DATE:		20160127
DATE AS OF CHANGE:		20160127

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			ZAFGEN, INC.
		CENTRAL INDEX KEY:			0001374690
		STANDARD INDUSTRIAL CLASSIFICATION:	PHARMACEUTICAL PREPARATIONS [2834]
		IRS NUMBER:				203857670
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		175 PORTLAND STREET
		STREET 2:		4TH FLOOR
		CITY:			BOSTON
		STATE:			MA
		ZIP:			02114
		BUSINESS PHONE:		617-622-4003

	MAIL ADDRESS:	
		STREET 1:		175 PORTLAND STREET
		STREET 2:		4TH FLOOR
		CITY:			BOSTON
		STATE:			MA
		ZIP:			02114

	FORMER COMPANY:	
		FORMER CONFORMED NAME:	ZAFGEN INC
		DATE OF NAME CHANGE:	20060906

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Barrett Peter
		CENTRAL INDEX KEY:			0001291895

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-36510
		FILM NUMBER:		161366438

	MAIL ADDRESS:	
		STREET 1:		C/O ALNYLAM PHARMACEUTICALS, INC.
		STREET 2:		300 THIRD STREET
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02142
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>doc4.xml
<DESCRIPTION>FORM 4 SUBMISSION
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2016-01-25</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001291895</rptOwnerCik>
            <rptOwnerName>Barrett Peter</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ATLAS VENTURE FUND VII, L.P.,</rptOwnerStreet1>
            <rptOwnerStreet2>25 FIRST STREET, SUITE 303</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02141</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2016-01-25</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>8849</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>7.91</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>4643327</value>
                    <footnoteId id="F2"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">These securities were issued in lieu of cash fees under the Non-Employee Director Compensation Policy pursuant to a Restricted Stock Agreement and the restrictions lapse over a period of one year starting January 1, 2016 on a quarterly basis in arrears.</footnote>
        <footnote id="F2">The Reporting Person previously reported 5,632,730 shares directly held by Atlas Venture Fund VII, L.P. (&quot;Atlas Venture&quot;).  On March 24, 2015, Atlas Venture distributed in-kind 1,000,000 shares pro rata to its limited partners. The Reporting Person now reports 4,632,730 shares directly held by Atlas Venture and disclaims beneficial ownership of all such shares except to the extent of his pecuniary interest, if any, therein.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Laurie Burlingame, Attorney-In-Fact</signatureName>
        <signatureDate>2016-01-27</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
