<?xml version="1.0"?>
<ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType><periodOfReport>2003-08-11</periodOfReport>
    <issuer>
        <issuerCik>0000716054</issuerCik>
        <issuerName>CYPRESS BIOSCIENCE INC</issuerName>
        <issuerTradingSymbol>cypb</issuerTradingSymbol></issuer><reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001055666</rptOwnerCik>
            <rptOwnerName>KRANZLER JAY D</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>4350 EXECUTIVE DRIVE, SUITE 325</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>SAN DIEGO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>92121</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
<isDirector>1</isDirector><isOfficer>1</isOfficer><isTenPercentOwner>0</isTenPercentOwner><isOther>0</isOther><officerTitle>Chief Executive Officer &amp; Sec.</officerTitle></reportingOwnerRelationship></reportingOwner><derivativeTable><derivativeTransaction><securityTitle><value>Stock Option (right to buy)</value></securityTitle><conversionOrExercisePrice><value>4.53</value></conversionOrExercisePrice><transactionDate><value>2003-08-11</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>A</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>500000</value></transactionShares><transactionPricePerShare><value>4.53</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2003-08-11</value><footnoteId id="F1"/></exerciseDate><expirationDate><value>2013-08-11</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>500000</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>500000</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></derivativeTransaction></derivativeTable><footnotes><footnote id="F1">The shares subject to the option vest daily and ratably over a period of four years beginning August 11, 2003.</footnote></footnotes><remarks/><ownerSignature><signatureName>Sabrina Martucci Johnson Attorney-in-Fact</signatureName><signatureDate>2003-08-13</signatureDate></ownerSignature></ownershipDocument>

