-----BEGIN PRIVACY-ENHANCED MESSAGE-----
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,
 FsUUNhNv+JxMXt2gIqFt89Y5pMq7sAFlcgXsC2uTpY2LROx73+IExVk7rzyxUZiB
 940JPorapMZ2QKlocbUMVQ==

<SEC-DOCUMENT>0001181431-04-002922.txt : 20040115
<SEC-HEADER>0001181431-04-002922.hdr.sgml : 20040115
<ACCEPTANCE-DATETIME>20040115192951
ACCESSION NUMBER:		0001181431-04-002922
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20040113
FILED AS OF DATE:		20040115

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:		04528349

	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>rrd29202.xml
<DESCRIPTION>FORM 4
<TEXT>
<XML>
<?xml version="1.0"?><ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType><periodOfReport>2004-01-13</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>2004-01-13</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>A</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>14000</value></transactionShares><transactionPricePerShare><value>1.625</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>62460</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership></ownershipNature></nonDerivativeTransact
ion><nonDerivativeTransaction><securityTitle><value>Common Stock</value><footnoteId id="F1"/></securityTitle><transactionDate><value>2004-01-13</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>S</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>14000</value></transactionShares><transactionPricePerShare><value>4.4614</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>48460</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership></ownershipNature></nonDerivativeTransaction><nonDerivativeTransaction><securityTitle><value>Common Stock</value><footnoteId id="F1"/></securityTitle><transactionDate><value>2004-01-14</value></transactionDate><t
ransactionCoding><transactionFormType>4</transactionFormType><transactionCode>A</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>29250</value></transactionShares><transactionPricePerShare><value>1.625</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>77710</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership></ownershipNature></nonDerivativeTransaction><nonDerivativeTransaction><securityTitle><value>Common Stock</value><footnoteId id="F1"/></securityTitle><transactionDate><value>2004-01-14</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>S</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionA
mounts><transactionShares><value>29250</value></transactionShares><transactionPricePerShare><value>5.085</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><value>1.625</value></conversionOrExercisePrice><transactionDate><value>2004-01-13</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>14000</value></transactionSh
ares><transactionPricePerShare><value>1.625</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>1995-12-11</value></exerciseDate><expirationDate><value>2004-03-31</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Shares</value></underlyingSecurityTitle><underlyingSecurityShares><value>14000</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>669716</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership></ownershipNature></derivativeTransaction><derivativeTransaction><securityTitle><value>Stock Options</value><footnoteId id="F1"/></securityTitle><conversionOrExercisePrice><value>1.625</value></conversionOrExercisePrice><transactionDate><value>2004-01-14</value></transactionDate><transactionCoding><transaction
FormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>29250</value></transactionShares><transactionPricePerShare><value>1.625</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>1995-12-11</value></exerciseDate><expirationDate><value>2004-03-31</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Shares</value></underlyingSecurityTitle><underlyingSecurityShares><value>29250</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>640466</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership></ownershipNature></derivativeTransaction></derivativeTable><footnotes><footnote id="F1">Please note that t
his 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>2004-01-15</signatureDate></ownerSignature></ownershipDocument>



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</SEC-DOCUMENT>
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