<SEC-DOCUMENT>0000899243-17-024381.txt : 20171017
<SEC-HEADER>0000899243-17-024381.hdr.sgml : 20171017
<ACCEPTANCE-DATETIME>20171017171152
ACCESSION NUMBER:		0000899243-17-024381
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20171013
FILED AS OF DATE:		20171017
DATE AS OF CHANGE:		20171017

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Heller Frances K
		CENTRAL INDEX KEY:			0001441724

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-36510
		FILM NUMBER:		171141224

	MAIL ADDRESS:	
		STREET 1:		249 E. GRAND AVENUE
		CITY:			S. SAN FRANCISCO
		STATE:			CA
		ZIP:			94083

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
</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>2017-10-13</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001441724</rptOwnerCik>
            <rptOwnerName>Heller Frances K</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ZAFGEN, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>175 PORTLAND STREET, 4TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>BOSTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02114</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2017-10-13</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>10000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>3.8988</value>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>47961</value>
                    <footnoteId id="F2"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">The price reported in Column 4 is a weighted average price. These shares were purchased in multiple transactions at prices ranging from $3.8645 to $3.92, inclusive. The reporting person undertakes to provide to Zafgen, Inc., any security holder of Zafgen, Inc., or the staff of the Securities and Exchange Commission, upon request, full information regarding the number of shares purchased at each separate price within the ranges set forth herein.</footnote>
        <footnote id="F2">Total number of shares includes 7,961 shares of Common Stock acquired by the Reporting Person on December 31, 2012 that were not previously reported.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Laurie Burlingame, Attorney-in-Fact</signatureName>
        <signatureDate>2017-10-17</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
