<SEC-DOCUMENT>0001356090-15-000069.txt : 20151204
<SEC-HEADER>0001356090-15-000069.hdr.sgml : 20151204
<ACCEPTANCE-DATETIME>20151204162308
ACCESSION NUMBER:		0001356090-15-000069
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20151202
FILED AS OF DATE:		20151204
DATE AS OF CHANGE:		20151204

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:			Krishnan Suma
		CENTRAL INDEX KEY:			0001298711

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-36042
		FILM NUMBER:		151270362

	MAIL ADDRESS:	
		STREET 1:		1861 PRATT DRIVE
		STREET 2:		SUITE 1090
		CITY:			BLACKSBURG
		STATE:			VA
		ZIP:			24060
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>edgar.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2015-12-02</periodOfReport>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001298711</rptOwnerCik>
            <rptOwnerName>Krishnan Suma</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--Product Development</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2015-12-02</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>20000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>35.913</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F3"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>42900</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2015-12-04</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>900</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>30.1233</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>42000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>42000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By spouse</value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">The price reported is a weighted average price. These shares were sold in multiple transactions at prices ranging from $35.78 to $36.25, inclusive. The reporting person undertakes to provide to Intrexon Corporation, any security holder of Intrexon Corporation, or the staff of the Securities and Exchange Commission, upon request, full information regarding the number of shares sold at each separate price within the price ranges set forth herein.</footnote>
        <footnote id="F2">The price reported is a weighted average price. These shares were sold in multiple transactions at prices ranging from $30.09 to $30.15, inclusive. The reporting person undertakes to provide to Intrexon Corporation, any security holder of Intrexon Corporation, or the staff of the Securities and Exchange Commission, upon request, full information regarding the number of shares sold at each separate price within the price ranges set forth herein.</footnote>
        <footnote id="F3">The shares of common stock sold in this transaction are jointly owned by the reporting person and the reporting person's spouse, Krish S. Krishnan, who is concurrently filing a Form 4 to report the sale of these jointly owned shares.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>Suma M. Krishnan, by Donald P. Lehr, Power of Attorney</signatureName>
        <signatureDate>2015-12-04</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
