<SEC-DOCUMENT>0000899243-18-000596.txt : 20180105
<SEC-HEADER>0000899243-18-000596.hdr.sgml : 20180105
<ACCEPTANCE-DATETIME>20180105170212
ACCESSION NUMBER:		0000899243-18-000596
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20180103
FILED AS OF DATE:		20180105
DATE AS OF CHANGE:		20180105

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Daniel Thomas O
		CENTRAL INDEX KEY:			0001538894

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-36510
		FILM NUMBER:		18514072

	MAIL ADDRESS:	
		STREET 1:		C/O CELGENE CORPORATION
		STREET 2:		86 MORRIS AVENUE
		CITY:			SUMMIT
		STATE:			NJ
		ZIP:			07901

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>2018-01-03</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001538894</rptOwnerCik>
            <rptOwnerName>Daniel Thomas O</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>2018-01-03</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>8687</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>5.18</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>19452</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">The common stock was 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, 2018 on quarterly basis in arrears.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Laurie Burlingame (Attorney-In-Fact)</signatureName>
        <signatureDate>2018-01-05</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
