<SEC-DOCUMENT>0001356090-16-000085.txt : 20160126
<SEC-HEADER>0001356090-16-000085.hdr.sgml : 20160126
<ACCEPTANCE-DATETIME>20160126215158
ACCESSION NUMBER:		0001356090-16-000085
CONFORMED SUBMISSION TYPE:	4/A
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20160107
FILED AS OF DATE:		20160126
DATE AS OF CHANGE:		20160126

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			INTREXON CORP
		CENTRAL INDEX KEY:			0001356090
		STANDARD INDUSTRIAL CLASSIFICATION:	SERVICES-COMMERCIAL PHYSICAL & BIOLOGICAL RESEARCH [8731]
		IRS NUMBER:				000000000
		STATE OF INCORPORATION:			VA
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		1750 KRAFT DRIVE
		STREET 2:		SUITE 1400
		CITY:			BLACKSBURG
		STATE:			VA
		ZIP:			24060
		BUSINESS PHONE:		301-556-9809

	MAIL ADDRESS:	
		STREET 1:		1750 KRAFT DRIVE
		STREET 2:		SUITE 1400
		CITY:			BLACKSBURG
		STATE:			VA
		ZIP:			24060

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Cratsenburg Ena Chan
		CENTRAL INDEX KEY:			0001663065

	FILING VALUES:
		FORM TYPE:		4/A
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-36042
		FILM NUMBER:		161362904

	MAIL ADDRESS:	
		STREET 1:		20374 SENECA MEADOWS PARKWAY
		CITY:			GERMANTOWN
		STATE:			MD
		ZIP:			20876
</SEC-HEADER>
<DOCUMENT>
<TYPE>4/A
<SEQUENCE>1
<FILENAME>edgar.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0306</schemaVersion>

    <documentType>4/A</documentType>

    <periodOfReport>2016-01-07</periodOfReport>

    <dateOfOriginalSubmission>2016-01-11</dateOfOriginalSubmission>

    <issuer>
        <issuerCik>0001356090</issuerCik>
        <issuerName>INTREXON CORP</issuerName>
        <issuerTradingSymbol>XON</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001663065</rptOwnerCik>
            <rptOwnerName>Cratsenburg Ena Chan</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>20374 SENECA MEADOWS PARKWAY</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>GERMANTOWN</rptOwnerCity>
            <rptOwnerState>MD</rptOwnerState>
            <rptOwnerZipCode>20876</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>SVP, Consumer Sector</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Option to Purchase Common Stock (Right to Buy)</value>
                <footnoteId id="F2"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>27.14</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2016-01-07</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>275000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2026-01-07</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>275000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>275000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">These options vest in 25% increments on January 7, 2017, 2018, 2019 and 2020.</footnote>
        <footnote id="F2">This Form 4 was filed timely but under the wrong reporting person CIK.  This amended Form 4 replaces the Form 4 filed on January 11, 2016 under accession number 0001356090-16-000078 in its entirety.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Ena Chan Cratsenburg, by Donald P. Lehr, Power of Attorney</signatureName>
        <signatureDate>2016-01-26</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
