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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4/A</documentType>

    <periodOfReport>2017-06-22</periodOfReport>

    <dateOfOriginalSubmission>2017-06-26</dateOfOriginalSubmission>

    <issuer>
        <issuerCik>0001359931</issuerCik>
        <issuerName>PROTEON THERAPEUTICS INC</issuerName>
        <issuerTradingSymbol>PRTO</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001599744</rptOwnerCik>
            <rptOwnerName>TVM Life Science Ventures VI GmbH &amp; Co KG</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O TVM CAPITAL GROUP</rptOwnerStreet1>
            <rptOwnerStreet2>OTTOSTRASSE 4</rptOwnerStreet2>
            <rptOwnerCity>MUNICH</rptOwnerCity>
            <rptOwnerState>2M</rptOwnerState>
            <rptOwnerZipCode>80333</rptOwnerZipCode>
            <rptOwnerStateDescription>GERMANY</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001318584</rptOwnerCik>
            <rptOwnerName>TVM Life Science Ventures VI LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O TVM CAPITAL GROUP</rptOwnerStreet1>
            <rptOwnerStreet2>OTTOSTRASSE 4</rptOwnerStreet2>
            <rptOwnerCity>MUNICH</rptOwnerCity>
            <rptOwnerState>2M</rptOwnerState>
            <rptOwnerZipCode>80333</rptOwnerZipCode>
            <rptOwnerStateDescription>GERMANY</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001398598</rptOwnerCik>
            <rptOwnerName>Birner Hubert</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O TVM CAPITAL GROUP</rptOwnerStreet1>
            <rptOwnerStreet2>OTTOSTRASSE 4</rptOwnerStreet2>
            <rptOwnerCity>MUNICH</rptOwnerCity>
            <rptOwnerState>2M</rptOwnerState>
            <rptOwnerZipCode>80333</rptOwnerZipCode>
            <rptOwnerStateDescription>GERMANY</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001398596</rptOwnerCik>
            <rptOwnerName>Fischer Stefan</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O TVM CAPITAL GROUP</rptOwnerStreet1>
            <rptOwnerStreet2>OTTOSTRASSE 4</rptOwnerStreet2>
            <rptOwnerCity>MUNICH</rptOwnerCity>
            <rptOwnerState>2M</rptOwnerState>
            <rptOwnerZipCode>80333</rptOwnerZipCode>
            <rptOwnerStateDescription>GERMANY</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001133921</rptOwnerCik>
            <rptOwnerName>SCHUHSLER HELMUT</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O TVM CAPITAL GROUP</rptOwnerStreet1>
            <rptOwnerStreet2>OTTOSTRASSE 4</rptOwnerStreet2>
            <rptOwnerCity>MUNICH</rptOwnerCity>
            <rptOwnerState>2M</rptOwnerState>
            <rptOwnerZipCode>80333</rptOwnerZipCode>
            <rptOwnerStateDescription>GERMANY</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Series A Convertible Preferred Stock</value>
                <footnoteId id="F1"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>.9949</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2017-06-22</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>372</value>
                    <footnoteId id="F2"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>1000.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F4"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock, $0.001 par value</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>373907</value>
                    <footnoteId id="F5"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>500</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">This amendment to the original Form 4 does not amend any item originally reported in Table II and the first line item of Table II is restated in this amendment for the sole purpose of gaining access to the electronic filing system; footnotes relating to such first line item are included for completeness and have not been amended.  This amendment is made by the Reporting Persons solely to include the power of attorney attached hereto as Exhibit 24.</footnote>
        <footnote id="F2">The shares are directly held by TVM Life Science Ventures VI GMBH &amp; Co. KG (&quot;TVM VI&quot;).  Hubert Birner (&quot;Birner&quot;), Stefan Fischer (&quot;Fischer&quot;), and Helmut Schuhsler (&quot;Schuhsler&quot;) are members of the investment committee of TVM Life Science Management VI L.P. (&quot;TVM VI Management&quot;), a special limited partner of TVM VI, with voting and dispositive power over the shares held by TVM VI.  TVM VI Management, Birner, Schuhsler and Fischer each disclaim beneficial ownership of the shares held by TVM VI, except to the extent of any pecuniary interest therein, if any.  Birner is a director of the issuer.</footnote>
        <footnote id="F3">The Series A convertible preferred stock (the &quot;Series A Stock&quot;) is convertible, at the option of the holder, into Proteon Therapeutics Inc. common stock, $0.01 par value per share (the &quot;Common Stock&quot;), at a price per share equal to $0.9949.</footnote>
        <footnote id="F4">The Series A Stock has no expiration date.</footnote>
        <footnote id="F5">The certificate of designations for the Series A Stock contains a provision prohibiting conversion to the extent that upon conversion the holder, together with its affiliates and any &quot;group&quot; members, would beneficially own in excess of 9.985% of the number of shares of Common Stock then outstanding.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Stefan Fischer, Director of TVM Life Science Ventures VI LLC, general partner of TVM Life Science Ventures Management VI L.P., managing limited partner of TVM Life Science Ventures VI GMBH &amp; Co. KG</signatureName>
        <signatureDate>2017-06-30</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Stefan Fischer, Director of TVM Life Science Ventures VI LLC, general partner of TVM Life Science Ventures Management VI L.P., managing limited partner of TVM Life Science Ventures VI L.P.</signatureName>
        <signatureDate>2017-06-30</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Stefan Fischer, by power of attorney for Hubert Birner</signatureName>
        <signatureDate>2017-06-30</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Stefan Fischer</signatureName>
        <signatureDate>2017-06-30</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Stefan Fischer, by power of attorney for Helmut Schuhsler</signatureName>
        <signatureDate>2017-06-30</signatureDate>
    </ownerSignature>
</ownershipDocument>
