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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
Originator-Key-Asymmetric:
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 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 GRBiEh8Bd+2ZQgbHnXUf+j5fm/2Mx6r/DsbVyhgfFn2dj0DqiKOXXmDdqp4ROR1z
 iJ96JOSIrpbjtslO/mA7ZA==

<SEC-DOCUMENT>0001181431-03-026241.txt : 20031009
<SEC-HEADER>0001181431-03-026241.hdr.sgml : 20031009
<ACCEPTANCE-DATETIME>20031009122104
ACCESSION NUMBER:		0001181431-03-026241
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20031007
FILED AS OF DATE:		20031009

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			HENNESSEY ROBERT J
		CENTRAL INDEX KEY:			0001234374

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-10824
		FILM NUMBER:		03934578

	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>rrd20148.xml
<DESCRIPTION>FORM 4
<TEXT>
<XML>
<?xml version="1.0"?><ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType><periodOfReport>2003-10-07</periodOfReport><notSubjectToSection16>0</notSubjectToSection16>
    <issuer>
        <issuerCik>0000356830</issuerCik>
        <issuerName>GENOME THERAPEUTICS CORP</issuerName>
        <issuerTradingSymbol>GENE</issuerTradingSymbol></issuer><reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001234374</rptOwnerCik>
            <rptOwnerName>HENNESSEY ROBERT J</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>100 BEAVER STREET</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>WALTHAM</rptOwnerCity>
            <rptOwnerState></rptOwnerState>
            <rptOwnerZipCode>02453</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
<isDirector>1</isDirector><isOfficer>0</isOfficer><isTenPercentOwner>0</isTenPercentOwner><isOther>0</isOther></reportingOwnerRelationship></reportingOwner><nonDerivativeTable><nonDerivativeTransaction><securityTitle><value>Common Stock</value><footnoteId id="F1"/></securityTitle><transactionDate><value>2003-10-07</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>A</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>8000</value></transactionShares><transactionPricePerShare><value>1.625</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>56460</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership></ownershipNature></nonDerivativeTransacti
on><nonDerivativeTransaction><securityTitle><value>Common Stock</value><footnoteId id="F1"/></securityTitle><transactionDate><value>2003-10-07</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>S</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>8000</value></transactionShares><transactionPricePerShare><value>2.75</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>48460</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership></ownershipNature></nonDerivativeTransaction></nonDerivativeTable><derivativeTable><derivativeTransaction><securityTitle><value>Stock Options</value><footnoteId id="F1"/></securityTitle><conversionOrExercisePrice><va
lue>1.625</value></conversionOrExercisePrice><transactionDate><value>2003-10-07</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>8000</value></transactionShares><transactionPricePerShare><value>1.625</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>1995-12-11</value></exerciseDate><expirationDate><value>2003-12-31</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Shares</value></underlyingSecurityTitle><underlyingSecurityShares><value>8000</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>787966</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value><
/directOrIndirectOwnership></ownershipNature></derivativeTransaction></derivativeTable><footnotes><footnote id="F1">Please note that this transaction occurred in accordance with the terms and conditions of a Rule 10b5-1 Trading Plan.</footnote></footnotes><ownerSignature><signatureName>Manny Bougoulas, Controller, by power of atty</signatureName><signatureDate>2003-10-09</signatureDate></ownerSignature></ownershipDocument>



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</TEXT>
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</SEC-DOCUMENT>
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