-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
 G6hFuGgTZ2yKVl9nEeGysWu+WET+ZzT+NZjhE6Y6LkCj1wcxWFQzgpmBKNvls1NF
 gCgeii+orDmFovPLjDRFCA==

<SEC-DOCUMENT>0001181431-04-017729.txt : 20040326
<SEC-HEADER>0001181431-04-017729.hdr.sgml : 20040326
<ACCEPTANCE-DATETIME>20040326184920
ACCESSION NUMBER:		0001181431-04-017729
CONFORMED SUBMISSION TYPE:	3
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20040227
FILED AS OF DATE:		20040326

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			PATOU GARY
		CENTRAL INDEX KEY:			0001283535

	FILING VALUES:
		FORM TYPE:		3
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-10824
		FILM NUMBER:		04694318

	BUSINESS ADDRESS:	
		STREET 1:		100 BEAVER ST
		CITY:			WALTHAM
		STATE:			MA
		ZIP:			02453
		BUSINESS PHONE:		6508371850

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			GENOME THERAPEUTICS CORP
		CENTRAL INDEX KEY:			0000356830
		STANDARD INDUSTRIAL CLASSIFICATION:	IN VITRO & IN VIVO DIAGNOSTIC SUBSTANCES [2835]
		IRS NUMBER:				042297484
		STATE OF INCORPORATION:			MA
		FISCAL YEAR END:			0831

	BUSINESS ADDRESS:	
		STREET 1:		1OO BEAVER ST
		CITY:			WALTHAM
		STATE:			MA
		ZIP:			02453
		BUSINESS PHONE:		7813982300

	MAIL ADDRESS:	
		STREET 1:		100 BEAVER STREET
		CITY:			WALTHAM
		STATE:			MA
		ZIP:			02453

	FORMER COMPANY:	
		FORMER CONFORMED NAME:	COLLABORATIVE RESEARCH INC
		DATE OF NAME CHANGE:	19920703
</SEC-HEADER>
<DOCUMENT>
<TYPE>3
<SEQUENCE>1
<FILENAME>rrd37586.xml
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0201</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2004-02-27</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0000356830</issuerCik>
        <issuerName>GENOME THERAPEUTICS CORP</issuerName>
        <issuerTradingSymbol>GENE</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001283535</rptOwnerCik>
            <rptOwnerName>PATOU GARY</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>100 BEAVER STREET</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>WALTHAM</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02453</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Chief Medical Officer</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Options (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.18</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2006-01-08</value>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2011-01-08</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>169646</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Options (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.18</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2005-12-12</value>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2011-12-12</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>42411</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Options (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>.07</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2007-02-10</value>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <value>2013-02-10</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>928463</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">A 5 year vesting period. 20% of the options will vest on the one year anniversary date of the grant .  The remaining options will vest monthly over the remaining four years of the vesting period.</footnote>
        <footnote id="F2">A 4 year vesting period. 20% of the options will vest on the one year anniversary date of the grant .  The remaining options will vest monthly over the remaining three years of the vesting period.</footnote>
        <footnote id="F3">A 4 year vesting period. 20% of the options will vest on the one year anniversary date of the grant .  The remaining options will vest monthly over the remaining three years of the vesting period.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Gary Patou</signatureName>
        <signatureDate>2004-03-26</signatureDate>
    </ownerSignature>
</ownershipDocument>

</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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