<SEC-DOCUMENT>0001225385-16-000084.txt : 20161205
<SEC-HEADER>0001225385-16-000084.hdr.sgml : 20161205
<ACCEPTANCE-DATETIME>20161205111405
ACCESSION NUMBER:		0001225385-16-000084
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20161201
FILED AS OF DATE:		20161205
DATE AS OF CHANGE:		20161205

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:			Hassan Fred
		CENTRAL INDEX KEY:			0001110744

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-36042
		FILM NUMBER:		162033032

	MAIL ADDRESS:	
		STREET 1:		C/O WARBURG PINCUS LLC
		STREET 2:		450 LEXINGTON AVENUE
		CITY:			NEW YORK
		STATE:			NY
		ZIP:			10017

	FORMER NAME:	
		FORMER CONFORMED NAME:	HASSAN FRED
		DATE OF NAME CHANGE:	20000330
</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>2016-12-01</periodOfReport>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001110744</rptOwnerCik>
            <rptOwnerName>Hassan Fred</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>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2016-12-01</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>6900</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>29.0241</value>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>6900</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </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 $28.86 to $29.14, inclusive. The reporting person undertakes to provide Intrexon Corporation (&quot;Intrexon&quot;), any security holder of Intrexon, 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 range set forth in this footnote.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Fred Hassan, by Donald P. Lehr, Power of Attorney</signatureName>
        <signatureDate>2016-12-05</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
