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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
 MW+23/2zpApRpDFACBi1oUxSc7aNJuXja/+Vts0MmhDodkSy4FLFIFC+NQtL1Ejj
 DNZZtxRQkCyZ9k7BxZpSiw==

<SEC-DOCUMENT>0001181431-03-030047.txt : 20031110
<SEC-HEADER>0001181431-03-030047.hdr.sgml : 20031110
<ACCEPTANCE-DATETIME>20031110164111
ACCESSION NUMBER:		0001181431-03-030047
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20031103
FILED AS OF DATE:		20031110

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			STONE DAVID K
		CENTRAL INDEX KEY:			0001248571

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-10824
		FILM NUMBER:		03988828

	BUSINESS ADDRESS:	
		STREET 1:		24 LIBERTY ST
		CITY:			ACTON
		STATE:			MA
		ZIP:			01720
		BUSINESS PHONE:		9782638776

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>rrd22338.xml
<TEXT>
<XML>
<?xml version="1.0"?><ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType><periodOfReport>2003-11-03</periodOfReport><notSubjectToSection16>0</notSubjectToSection16>
    <issuer>
        <issuerCik>0000356830</issuerCik>
        <issuerName>GENOME THERAPEUTICS CORP</issuerName>
        <issuerTradingSymbol>GENE</issuerTradingSymbol></issuer><reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001248571</rptOwnerCik>
            <rptOwnerName>STONE DAVID K</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>100 BEAVER STREET</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>WALTHAM</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02453</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
<isDirector>1</isDirector><isOfficer>0</isOfficer><isTenPercentOwner>0</isTenPercentOwner><isOther>0</isOther></reportingOwnerRelationship></reportingOwner><derivativeTable><derivativeTransaction><securityTitle><value>Stock Options</value></securityTitle><conversionOrExercisePrice><value>.89</value></conversionOrExercisePrice><transactionDate><value>2003-11-03</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>A</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>303</value></transactionShares><transactionPricePerShare><value>0</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2003-11-03</value></exerciseDate><expirationDate><value>2013-11-03</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Shares</value></underlyingSecurityTitle><underlyingSe
curityShares><value>303</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>84015</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership></ownershipNature></derivativeTransaction><derivativeTransaction><securityTitle><value>Stock Options</value></securityTitle><conversionOrExercisePrice><value>.93</value></conversionOrExercisePrice><transactionDate><value>2003-11-06</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>A</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>922</value></transactionShares><transactionPricePerShare><value>0</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2003-11-06</value></exerciseDat
e><expirationDate><value>2013-11-06</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Shares</value></underlyingSecurityTitle><underlyingSecurityShares><value>922</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>84937</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership></ownershipNature></derivativeTransaction></derivativeTable><remarks>11/3/2003 - Compensation for attending audit committee meeting.

11/6/2003 - Compensation for attending quarterly directors meeting.</remarks><ownerSignature><signatureName>Manny Bougoulas, Corporate Controller, by power of atty</signatureName><signatureDate>2003-11-10</signatureDate></ownerSignature></ownershipDocument>



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