<SEC-DOCUMENT>0000899243-19-010033.txt : 20190404
<SEC-HEADER>0000899243-19-010033.hdr.sgml : 20190404
<ACCEPTANCE-DATETIME>20190404183707
ACCESSION NUMBER:		0000899243-19-010033
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20190402
FILED AS OF DATE:		20190404
DATE AS OF CHANGE:		20190404

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Singhal Priya
		CENTRAL INDEX KEY:			0001769608

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-36510
		FILM NUMBER:		19733183

	MAIL ADDRESS:	
		STREET 1:		C/O ZAFGEN, INC.
		STREET 2:		175 PORTLAND STREET 4TH FL
		CITY:			BOSTON
		STATE:			MA
		ZIP:			02114

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>2019-04-02</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001769608</rptOwnerCik>
            <rptOwnerName>Singhal Priya</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ZAFGEN, INC., 4TH FLOOR</rptOwnerStreet1>
            <rptOwnerStreet2>175 PORTLAND STREET</rptOwnerStreet2>
            <rptOwnerCity>BOSTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02114</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Head of Research &amp; Development</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>2.89</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2019-04-02</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>375000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2029-03-03</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>375000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>375000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">25% of this option vests on March 4, 2020, and the remainder vests in equal monthly installments thereafter over 36 months. The option has been granted pursuant to an inducement award agreement outside of the company's 2014 Stock Option and Incentive Plan as a material inducement to the reporting person's acceptance of employment with the company in accordance with NASDAQ Listing Rule 5635(c)(4). The option is subject to acceleration upon a change in control.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Shoaib Ghias, Attorney-In-Fact</signatureName>
        <signatureDate>2019-04-04</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
