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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
 DoM0ugA4pfEGmxaJxao+u4mflj/xD5uWBm30CEjpLr7hGGAnl8CAkeKiNj4ErDBf
 SgVDV1Pm+W7yRz3wfvGJdA==

<SEC-DOCUMENT>0001327363-06-000008.txt : 20060518
<SEC-HEADER>0001327363-06-000008.hdr.sgml : 20060518
<ACCEPTANCE-DATETIME>20060518164147
ACCESSION NUMBER:		0001327363-06-000008
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20060516
FILED AS OF DATE:		20060518
DATE AS OF CHANGE:		20060518

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			AUTOIMMUNE INC
		CENTRAL INDEX KEY:			0000879106
		STANDARD INDUSTRIAL CLASSIFICATION:	BIOLOGICAL PRODUCTS (NO DIAGNOSTIC SUBSTANCES) [2836]
		IRS NUMBER:				133489062
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		1199 MADIA STREET
		CITY:			PASADENA
		STATE:			CA
		ZIP:			91103
		BUSINESS PHONE:		6267921235

	MAIL ADDRESS:	
		STREET 1:		1199 MADIA STREET
		CITY:			PASADENA
		STATE:			CA
		ZIP:			91103

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			FERGUSON ALLAN R
		CENTRAL INDEX KEY:			0001030573
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-20948
		FILM NUMBER:		06852586

	BUSINESS ADDRESS:	
		BUSINESS PHONE:		6178599290

	MAIL ADDRESS:	
		STREET 1:		C/O ATLAS VENTURE
		STREET 2:		222 BERKELEY STREET
		CITY:			BOSTON
		STATE:			MA
		ZIP:			02116
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>edgar.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2006-05-16</periodOfReport>

    <issuer>
        <issuerCik>0000879106</issuerCik>
        <issuerName>AUTOIMMUNE INC</issuerName>
        <issuerTradingSymbol>AIMM</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001030573</rptOwnerCik>
            <rptOwnerName>FERGUSON ALLAN R</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>3I CORPORATION</rptOwnerStreet1>
            <rptOwnerStreet2>880 WINTER STREET, SUITE 330</rptOwnerStreet2>
            <rptOwnerCity>WALTHAM</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02451</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
                <footnoteId id="F1"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.30</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2006-05-16</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>6500</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2016-05-16</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>6500</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>6500</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The option replaces an option granted to Mr. Ferguson on May 15, 1996, which expired on May 15, 2006.</footnote>
        <footnote id="F2">The option is exercisable in four equal installments beginning on the first anniversary of the grant date.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Jennifer M. Adams, as attorney-in-fact</signatureName>
        <signatureDate>2006-05-18</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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