<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2006-12-29</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001004960</issuerCik>
        <issuerName>CONNETICS CORP</issuerName>
        <issuerTradingSymbol>CNCT</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001237556</rptOwnerCik>
            <rptOwnerName>FOEHR MATTHEW W</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>3160 PORTER DRIVE</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>PALO ALTO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94304</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Sr. VP Technical Operations</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, Par Value $0.001</value>
            </securityTitle>
            <transactionDate>
                <value>2006-12-29</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>5929</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>17.50</value>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, Par Value $0.001</value>
            </securityTitle>
            <transactionDate>
                <value>2006-12-29</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>38730</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>17.50</value>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Option to Purchase Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>12.45</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2006-12-29</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>9200</value>
                    <footnoteId id="F3"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>5.05</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2006-12-29</value>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <value>2013-01-02</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>9200</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">In connection with the merger agreement between issuer and Stiefel Laboratories, shares of the Issuer's common stock were converted into the right to receive $17.50 per share in cash, without interest.</footnote>
        <footnote id="F2">Immediately prior to the effective time of the merger between issuer and Stiefel Laboratories, Inc., all restrictions on these shares of restricted stock were released, and the shares became fully vested and eligible for the merger consideration in an amount equal to $17.50 multiplied by the number of shares of common stock subject to the restrictions, less any required witholding.</footnote>
        <footnote id="F3">Immediately prior to the effective time of the merger between issuer and Stiefel Laboratories, the options became fully vested.  In exchange for the options, the Issuer paid to the Reporting Person either (a) -0- for each grant of options if the exercise price of the options was equal to or greater than the merger consideration of $17.50, or (b) an amount equal to the excess of the merger consideration ($17.50) over the exercise price multiplied by the number of shares of common stock subject to the option, less any required witholding, if the exercise price of the option was less than the merger consideration of $17.50.</footnote>
        <footnote id="F4">The stock options were granted under a Connetics Corporation stock option plan and, but for the merger between Issuer and Stiefel Laboratories, would have been exercisable at the rate of 25% on the one year anniversary and 1/48 per month thereafter.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>Matthew W. Foehr</signatureName>
        <signatureDate>2007-01-03</signatureDate>
    </ownerSignature>
</ownershipDocument>
