<SEC-DOCUMENT>0001209191-14-043837.txt : 20140627
<SEC-HEADER>0001209191-14-043837.hdr.sgml : 20140627
<ACCEPTANCE-DATETIME>20140626162347
ACCESSION NUMBER:		0001209191-14-043837
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20140624
FILED AS OF DATE:		20140626
DATE AS OF CHANGE:		20140626

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:		ONE BROADWAY, 8TH FLOOR
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02142
		BUSINESS PHONE:		(617 ) 401-3051

	MAIL ADDRESS:	
		STREET 1:		ONE BROADWAY, 8TH FLOOR
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02142

	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:		14942961

	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>
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    <periodOfReport>2014-06-24</periodOfReport>

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        <issuerName>ZAFGEN, INC.</issuerName>
        <issuerTradingSymbol>ZFGN</issuerTradingSymbol>
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            <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>
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        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
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        </nonDerivativeTransaction>
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    <derivativeTable>
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            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
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                    <value>4768001</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
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                <transactionAcquiredDisposedCode>
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                <footnoteId id="F2"/>
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                <footnoteId id="F2"/>
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            <underlyingSecurity>
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                </underlyingSecurityTitle>
                <underlyingSecurityShares>
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                </underlyingSecurityShares>
            </underlyingSecurity>
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            <securityTitle>
                <value>Series D Preferred Stock</value>
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    <footnotes>
        <footnote id="F1">The Series A Preferred Stock automatically converted into Common Stock on a 6.28-for-1 basis at the closing of the Issuer's initial public offering for no consideration, and had no expiration date.</footnote>
        <footnote id="F2">The Series B Preferred Stock automatically converted into Common Stock on a 6.28-for-1 basis at the closing of the Issuer's initial public offering for no consideration, and had no expiration date.</footnote>
        <footnote id="F3">The Series C Preferred Stock automatically converted into Common Stock on a 6.28-for-1 basis at the closing of the Issuer's initial public offering for no consideration, and had no expiration date.</footnote>
        <footnote id="F4">The Series D Preferred Stock automatically converted into Common Stock on a 6.28-for-1 basis at the closing of the Issuer's initial public offering for no consideration, and had no expiration date.</footnote>
        <footnote id="F5">The securities are directly held by Atlas Venture Fund VII, L.P.(&quot;AV VII LP&quot;). The general partner of AV VII LP is Atlas Venture Associates VII, L.P. (&quot;AVA VII LP&quot;). The general partner of AVA VII LP is Atlas Venture Associates VII, Inc. The Reporting Person disclaims beneficial ownership of all shares except to the extent of his pecuniary interest, if any, therein.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Peter Barrett</signatureName>
        <signatureDate>2014-06-26</signatureDate>
    </ownerSignature>
</ownershipDocument>
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</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
