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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2012-07-25</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001386858</issuerCik>
        <issuerName>HYPERION THERAPEUTICS INC</issuerName>
        <issuerTradingSymbol>HPTX</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001436021</rptOwnerCik>
            <rptOwnerName>Panorama Capital, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>2440 SAND HILL ROAD, SUITE 302</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>MENLO PARK</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94025</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Series C-2 Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>831410</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Common Stock Warrant (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>4.08</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <value>2021-04-01</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>68986</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Preferred Stock Warrant (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>9.62</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <value>2018-10-25</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Series C-2 Convertible Preferred Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>29615</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Preferred Stock Warrant (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>9.62</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <value>2019-02-07</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Series C-2 Convertible Preferred Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>29615</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The reported securities are convertible at any time, in whole or in part, at the option of the Reporting Person, have no expiration date, and will convert into shares of common stock immediately prior to the closing of the Issuer's initial public offering.</footnote>
        <footnote id="F2">Panorama Capital, L.P. (&quot;Panorama&quot;) and Panorama Capital Management, LLC (&quot;PCM&quot;) are deemed to be a &quot;group&quot; for the purpose of Section 13(d) of the Securities Exchange Act of 1934, as amended.  PCM is the general partner of Panorama and the Managing Members of PCM, Christopher J. Albinson, Rodney A. Ferguson, Shahan D. Soghikian, and Damion Wicker, have sole voting and dispositive powers with respect to the securities held by Panorama.</footnote>
        <footnote id="F3">The warrants are not currently exercisable. Immediately prior to the closing of the Issuer's initial public offering, the warrants will automatically net exercise by their terms, which allows the Reporting Person to pay the exercise price of the warrant by forfeiting a portion of the exercised warrant shares with a value equal to the aggregate exercise price.  The warrants terminate if they are not exercised prior to the closing of the Issuer's initial public offering.</footnote>
        <footnote id="F4">The warrants are not currently exercisable. Immediately prior to the closing of the Issuer's initial public offering, the warrants will automatically net exercise by their terms, which allows the Reporting Person to pay the exercise price of the warrant by forfeiting a portion of the exercised warrant shares with a value equal to the aggregate exercise price.  The shares of Series C-2 Convertible Preferred Stock issuable upon exercise of the warrants will convert into shares of common stock upon the closing of the Issuer's initial public offering. The warrants terminate if they are not exercised prior to the closing of the Issuer's initial public offering.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Laura A. Berezin, Attorney-in-Fact</signatureName>
        <signatureDate>2012-07-25</signatureDate>
    </ownerSignature>
</ownershipDocument>
