-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
Originator-Key-Asymmetric:
 MFgwCgYEVQgBAQICAf8DSgAwRwJAW2sNKK9AVtBzYZmr6aGjlWyK3XmZv3dTINen
 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 NixOCJ6lQSd77d+8jh3nbycOTHdjmEb7uqUm0IWw6wbICFjYZnlWMvbciUEiXseP
 KXVCz8Q33sspIRIbKfAvkQ==

<SEC-DOCUMENT>0001335038-06-000001.txt : 20060202
<SEC-HEADER>0001335038-06-000001.hdr.sgml : 20060202
<ACCEPTANCE-DATETIME>20060202161337
ACCESSION NUMBER:		0001335038-06-000001
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20060131
FILED AS OF DATE:		20060202
DATE AS OF CHANGE:		20060202

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Fellows Lindon M
		CENTRAL INDEX KEY:			0001335038

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-21379
		FILM NUMBER:		06573807

	BUSINESS ADDRESS:	
		BUSINESS PHONE:		978-352-6220

	MAIL ADDRESS:	
		STREET 1:		26 HOVEY'S POND DRIVE
		CITY:			BOXFORD
		STATE:			MA
		ZIP:			01921

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			CUBIST PHARMACEUTICALS INC
		CENTRAL INDEX KEY:			0000912183
		STANDARD INDUSTRIAL CLASSIFICATION:	PHARMACEUTICAL PREPARATIONS [2834]
		IRS NUMBER:				223192085
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		65 HAYDEN AVENUE
		CITY:			LEXINGTON
		STATE:			MA
		ZIP:			02421
		BUSINESS PHONE:		781-860-8660

	MAIL ADDRESS:	
		STREET 1:		24 EMILY ST
		CITY:			CAMBRIDGE
		STATE:			MA
		ZIP:			02139
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>doc.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2006-01-31</periodOfReport>

    <issuer>
        <issuerCik>0000912183</issuerCik>
        <issuerName>CUBIST PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>CBST</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001335038</rptOwnerCik>
            <rptOwnerName>Fellows Lindon M</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>26 HOVEY'S POND DRIVE</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>BOXFORD</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>01921</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Senior Vice President</officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Options (Right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>21.61</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2006-01-31</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>10000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2006-04-30</value>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2016-01-31</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>10000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>10000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Option vests 6.25% quarterly over a four-year period.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>Christopher D.T. Guiffre, Esq. - Attorney in fact</signatureName>
        <signatureDate>2006-02-02</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
-----END PRIVACY-ENHANCED MESSAGE-----