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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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<SEC-DOCUMENT>0001181431-04-006889.txt : 20040205
<SEC-HEADER>0001181431-04-006889.hdr.sgml : 20040205
<ACCEPTANCE-DATETIME>20040205193227
ACCESSION NUMBER:		0001181431-04-006889
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20040204
FILED AS OF DATE:		20040205

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

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			COHEN STEPHEN
		CENTRAL INDEX KEY:			0001234372

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-10824
		FILM NUMBER:		04571350

	BUSINESS ADDRESS:	
		STREET 1:		100 BEAVER STREET
		CITY:			WALTHAM
		STATE:			MA
		ZIP:			02453
		BUSINESS PHONE:		7813982311
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>rrd31785.xml
<DESCRIPTION>FORM 4
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2004-02-04</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001234372</rptOwnerCik>
            <rptOwnerName>COHEN STEPHEN</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>100 BEAVER STREET</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>WALTHAM</rptOwnerCity>
            <rptOwnerState></rptOwnerState>
            <rptOwnerZipCode>02453-8443</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>SVP and CFO</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.9275</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2004-02-04</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>6128</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>6.425</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2004-02-04</value>
            </exerciseDate>
            <expirationDate>
                <value>2014-02-04</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>6128</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>239470</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.9275</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2004-02-04</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>6128</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>6.425</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2005-02-04</value>
            </exerciseDate>
            <expirationDate>
                <value>2014-02-04</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>6128</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>245598</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <remarks>Issuance of stock option under the Company's incentive bunus plan.</remarks>

    <ownerSignature>
        <signatureName>Stephen Cohen</signatureName>
        <signatureDate>2004-02-05</signatureDate>
    </ownerSignature>
</ownershipDocument>

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