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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
 W0AHdyFFyFpdwgFNwJaE+vB5VVWzRxD9W+yzij9TJACmLuiNbxbaPTbmRxGTobbk
 WCwONVf3WS5FJr9uJysdTg==

<SEC-DOCUMENT>0001181431-04-000676.txt : 20040105
<SEC-HEADER>0001181431-04-000676.hdr.sgml : 20040105
<ACCEPTANCE-DATETIME>20040105153610
ACCESSION NUMBER:		0001181431-04-000676
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20031231
FILED AS OF DATE:		20040105

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:		04504565

	BUSINESS ADDRESS:	
		STREET 1:		100 BEAVER STREET
		CITY:			WALTHAM
		STATE:			MA
		ZIP:			02453
		BUSINESS PHONE:		7813982311

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>4
<SEQUENCE>1
<FILENAME>rrd27818.xml
<TEXT>
<XML>
<?xml version="1.0"?><ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType><periodOfReport>2003-12-31</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><nonDerivativeTable><nonDerivativeTransaction><securityTitle><value>Common Shares</value><footnoteId id="F1"/></securityTitle><transactionDate><value>2003-12-31</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>J</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>4901</value></transactionShares><transactionPricePerShare><value>2.1675</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>23950</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership>
</ownershipNature></nonDerivativeTransaction></nonDerivativeTable><footnotes><footnote id="F1">The shares were issued under the Company's Employee Stock Purchase Plan</footnote></footnotes><ownerSignature><signatureName>Stephen Cohen</signatureName><signatureDate>2004-01-05</signatureDate></ownerSignature></ownershipDocument>



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</SEC-DOCUMENT>
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