-----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,
 FsYsWpd98ZxDQL/pO2CHauDvbCpu8UI86QZzGxnacwkmkDdkFWsMQwIhX8N/0dvd
 L8CGFzL8SBc7QxH/dTS15Q==

<SEC-DOCUMENT>0001181431-03-010862.txt : 20030616
<SEC-HEADER>0001181431-03-010862.hdr.sgml : 20030616
<ACCEPTANCE-DATETIME>20030616130745
ACCESSION NUMBER:		0001181431-03-010862
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20030612
FILED AS OF DATE:		20030616

REPORTING-OWNER:	

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

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-10824
		FILM NUMBER:		03745048

	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>rrd11039.xml
<DESCRIPTION>FORM 4
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>
    <schemaVersion>X0101</schemaVersion>

    <documentType>4</documentType>
<periodOfReport>2003-06-12</periodOfReport>
<notSubjectToSection16>0</notSubjectToSection16>
    <issuer>
        <issuerCik>0000356830</issuerCik>
        <issuerName>GENOME THERAPEUTICS CORP</issuerName>
        <issuerTradingSymbol>GENE</issuerTradingSymbol></issuer>
<reportingOwner>
<reportingOwnerId>
            <rptOwnerCik>0001234374</rptOwnerCik>
            <rptOwnerName>HENNESSSEY ROBERT J</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>  </rptOwnerStreet1>
            <rptOwnerStreet2>  </rptOwnerStreet2>
            <rptOwnerCity>  </rptOwnerCity>
            <rptOwnerState>  </rptOwnerState>
            <rptOwnerZipCode>  </rptOwnerZipCode>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
<isDirector>1</isDirector>
<isOfficer>0</isOfficer>
<isTenPercentOwner>0</isTenPercentOwner>
<isOther>0</isOther>
<officerTitle></officerTitle>
<otherText></otherText></reportingOwnerRelationship></reportingOwner>
<nonDerivativeSecurity>
<securityTitle>
<value>Common Stock</value>
<footnoteId id="F1"/></securityTitle>
<transactionDate>
<value>2003-06-12</value></transactionDate>
<transactionCoding>
<transactionFormType>4</transactionFormType>
<transactionCode>A</transactionCode>
<equitySwapInvolved>0</equitySwapInvolved></transactionCoding>
<transactionTimeliness>
<value></value></transactionTimeliness>
<transactionAmounts>
<transactionShares>
<value>10000</value></transactionShares>
<transactionValue>
<value>1.625</value></transactionValue>
<transactionAcquiredDisposedCode>
<value>A</value></transactionAcquiredDisposedCode></transactionAmounts>
<postTransactionAmounts>
<sharesOwnedFollowingTransaction>
<value>58460</value></sharesOwnedFollowingTransaction></postTransactionAmounts>
<ownershipNature>
<directOrIndirectOwnership>
<value>D</value></directOrIndirectOwnership>
<natureOfOwnership>
<value></value></natureOfOwnership></ownershipNature></nonDerivativeSecurity>
<nonDerivativeSecurity>
<securityTitle>
<value>Common Stock</value>
<footnoteId id="F1"/></securityTitle>
<transactionDate>
<value>2003-06-12</value></transactionDate>
<transactionCoding>
<transactionFormType>4</transactionFormType>
<transactionCode>S</transactionCode>
<equitySwapInvolved>0</equitySwapInvolved></transactionCoding>
<transactionTimeliness>
<value></value></transactionTimeliness>
<transactionAmounts>
<transactionShares>
<value>10000</value></transactionShares>
<transactionValue>
<value>3.601</value></transactionValue>
<transactionAcquiredDisposedCode>
<value>D</value></transactionAcquiredDisposedCode></transactionAmounts>
<postTransactionAmounts>
<sharesOwnedFollowingTransaction>
<value>48460</value></sharesOwnedFollowingTransaction></postTransactionAmounts>
<ownershipNature>
<directOrIndirectOwnership>
<value>D</value></directOrIndirectOwnership>
<natureOfOwnership>
<value></value></natureOfOwnership></ownershipNature></nonDerivativeSecurity>
<nonDerivativeSecurity>
<securityTitle>
<value>Common Stock</value>
<footnoteId id="F1"/></securityTitle>
<transactionDate>
<value>2003-06-13</value></transactionDate>
<transactionCoding>
<transactionFormType>4</transactionFormType>
<transactionCode>A</transactionCode>
<equitySwapInvolved>0</equitySwapInvolved></transactionCoding>
<transactionTimeliness>
<value></value></transactionTimeliness>
<transactionAmounts>
<transactionShares>
<value>5000</value></transactionShares>
<transactionValue>
<value>1.625</value></transactionValue>
<transactionAcquiredDisposedCode>
<value>A</value></transactionAcquiredDisposedCode></transactionAmounts>
<postTransactionAmounts>
<sharesOwnedFollowingTransaction>
<value>53460</value></sharesOwnedFollowingTransaction></postTransactionAmounts>
<ownershipNature>
<directOrIndirectOwnership>
<value>D</value></directOrIndirectOwnership>
<natureOfOwnership>
<value></value></natureOfOwnership></ownershipNature></nonDerivativeSecurity>
<nonDerivativeSecurity>
<securityTitle>
<value>Common Stock</value>
<footnoteId id="F1"/></securityTitle>
<transactionDate>
<value>2003-06-13</value></transactionDate>
<transactionCoding>
<transactionFormType>4</transactionFormType>
<transactionCode>S</transactionCode>
<equitySwapInvolved>0</equitySwapInvolved></transactionCoding>
<transactionTimeliness>
<value></value></transactionTimeliness>
<transactionAmounts>
<transactionShares>
<value>5000</value></transactionShares>
<transactionValue>
<value>3.296</value></transactionValue>
<transactionAcquiredDisposedCode>
<value>D</value></transactionAcquiredDisposedCode></transactionAmounts>
<postTransactionAmounts>
<sharesOwnedFollowingTransaction>
<value>48460</value></sharesOwnedFollowingTransaction></postTransactionAmounts>
<ownershipNature>
<directOrIndirectOwnership>
<value>D</value></directOrIndirectOwnership>
<natureOfOwnership>
<value></value></natureOfOwnership></ownershipNature></nonDerivativeSecurity>
<derivativeSecurity>
<securityTitle>
<value>Stock Options</value>
<footnoteId id="F1"/></securityTitle>
<conversionOrExercisePrice>
<value>1.625</value></conversionOrExercisePrice>
<transactionDate>
<value>2003-06-12</value></transactionDate>
<transactionCoding>
<transactionFormType>4</transactionFormType>
<transactionCode>M</transactionCode>
<equitySwapInvolved>0</equitySwapInvolved></transactionCoding>
<transactionAmounts>
<transactionShares>
<value>10000</value></transactionShares>
<transactionValue>
<value>1.625</value></transactionValue>
<transactionAcquiredDisposedCode>
<value>D</value></transactionAcquiredDisposedCode></transactionAmounts>
<exerciseDate>
<value>1995-12-11</value></exerciseDate>
<expirationDate>
<value>2003-09-30</value></expirationDate>
<underlyingSecurity>
<underlyingSecurityTitle>
<value>Common Shares</value></underlyingSecurityTitle>
<underlyingSecurityShares>
<value>10000</value></underlyingSecurityShares></underlyingSecurity>
<postTransactionAmounts>
<sharesOwnedFollowingTransaction>
<value>945466</value></sharesOwnedFollowingTransaction></postTransactionAmounts>
<ownershipNature>
<directOrIndirectOwnership>
<value>D</value></directOrIndirectOwnership>
<natureOfOwnership>
<value></value></natureOfOwnership></ownershipNature></derivativeSecurity>
<derivativeSecurity>
<securityTitle>
<value>Stock Options</value>
<footnoteId id="F1"/></securityTitle>
<conversionOrExercisePrice>
<value>1.625</value></conversionOrExercisePrice>
<transactionDate>
<value>2003-06-13</value></transactionDate>
<transactionCoding>
<transactionFormType>4</transactionFormType>
<transactionCode>M</transactionCode>
<equitySwapInvolved>0</equitySwapInvolved></transactionCoding>
<transactionAmounts>
<transactionShares>
<value>5000</value></transactionShares>
<transactionValue>
<value>1.625</value></transactionValue>
<transactionAcquiredDisposedCode>
<value>D</value></transactionAcquiredDisposedCode></transactionAmounts>
<exerciseDate>
<value>1995-12-11</value></exerciseDate>
<expirationDate>
<value>2003-09-30</value></expirationDate>
<underlyingSecurity>
<underlyingSecurityTitle>
<value>Common Shares</value></underlyingSecurityTitle>
<underlyingSecurityShares>
<value>5000</value></underlyingSecurityShares></underlyingSecurity>
<postTransactionAmounts>
<sharesOwnedFollowingTransaction>
<value>940466</value></sharesOwnedFollowingTransaction></postTransactionAmounts>
<ownershipNature>
<directOrIndirectOwnership>
<value>D</value></directOrIndirectOwnership>
<natureOfOwnership>
<value></value></natureOfOwnership></ownershipNature></derivativeSecurity>
<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>2003-06-16</signatureDate></ownerSignature></ownershipDocument>


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