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

    <schemaVersion>X0202</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2006-12-14</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001373671</issuerCik>
        <issuerName>Isilon Systems, Inc.</issuerName>
        <issuerTradingSymbol>ISLN</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001103543</rptOwnerCik>
            <rptOwnerName>MADRONA VENTURE FUND I-A L P</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>1000 SECOND AVENUE</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3700</rptOwnerStreet2>
            <rptOwnerCity>SEATTLE</rptOwnerCity>
            <rptOwnerState>WA</rptOwnerState>
            <rptOwnerZipCode>98104</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001103465</rptOwnerCik>
            <rptOwnerName>MADRONA VENTURE FUND I-B, LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>1000 SECOND AVENUE</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3700</rptOwnerStreet2>
            <rptOwnerCity>SEATTLE</rptOwnerCity>
            <rptOwnerState>WA</rptOwnerState>
            <rptOwnerZipCode>98104</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001107551</rptOwnerCik>
            <rptOwnerName>MADRONA MANAGING DIRECTOR FUND, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>1000 SECOND AVENUE</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3700</rptOwnerStreet2>
            <rptOwnerCity>SEATTLE</rptOwnerCity>
            <rptOwnerState>WA</rptOwnerState>
            <rptOwnerZipCode>98104</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001382421</rptOwnerCik>
            <rptOwnerName>Madrona Investment Partners, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>1000 SECOND AVENUE</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3700</rptOwnerStreet2>
            <rptOwnerCity>SEATTLE</rptOwnerCity>
            <rptOwnerState>WA</rptOwnerState>
            <rptOwnerZipCode>98104</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Series A Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F2"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>2990473</value>
                    <footnoteId id="F3"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F4"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series B Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F2"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>2697184</value>
                    <footnoteId id="F3"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series C Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F2"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>2352684</value>
                    <footnoteId id="F3"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F6"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series D Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F2"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1670154</value>
                    <footnoteId id="F3"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F7"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series E Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F2"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>298643</value>
                    <footnoteId id="F3"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F8"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">These shares of Preferred Stock will automatically convert into shares of Common Stock upon the closing of the Issuer's initial public offering on a 1-for-1 basis.</footnote>
        <footnote id="F2">Not applicable.</footnote>
        <footnote id="F3">Reflects a 1-for-2.4 reverse stock split effected immediately prior to the filing date.  These shares of Preferred Stock will automatically convert into shares of Common Stock upon the closing of the Issuer's initial public offering on a 1-for-1 basis.</footnote>
        <footnote id="F4">Includes 2,411,195 shares held by Madrona Venture Fund I-A, LP (&quot;Madrona Venture Fund A&quot;), 262,430 shares held by Madrona Venture Fund I-B, LP (&quot;Madrona Venture Fund B&quot;) and 316,848 shares held by Madrona Managing Director Fund LLC (&quot;Madrona Managing Director Fund&quot;).  Matthew McIlwain (who is a director of the Issuer and files separate Section 16(a) reports) is a managing director of various entities affiliated with Madrona.  Madrona Investment Partners, LLC is the general partner of Madrona Venture Fund A and Madrona Venture Fund B.  Each of the Filing Persons disclaims beneficial ownership of the shares except to the extent of his or its pecuniary interest therein.</footnote>
        <footnote id="F5">Includes 2,174,726 shares held by Madrona Venture Fund A, 236,688 shares held by Madrona Venture Fund B and 285,770 shares held by Madrona Managing Director Fund.  Each of the Filing Persons disclaims beneficial ownership of the shares except to the extent of his or its pecuniary interest therein.</footnote>
        <footnote id="F6">Includes 1,896,958 shares held by Madrona Venture Fund A, 206,456 shares held by Madrona Venture Fund B and 249,270 shares held by Madrona Managing Director Fund.  Each of the Filing Persons disclaims beneficial ownership of the shares except to the extent of his or its pecuniary interest therein.</footnote>
        <footnote id="F7">Includes 1,346,637 shares held by Madrona Venture Fund A, 146,562 shares held by Madrona Venture Fund B and 176,955 shares held by Madrona Managing Director Fund.  Each of the Filing Persons disclaims beneficial ownership of the shares except to the extent of his or its pecuniary interest therein.</footnote>
        <footnote id="F8">Includes 240,795 shares held by Madrona Venture Fund A, 26,207 shares held by Madrona Venture Fund B and 31,641 shares held by Madrona Managing Director Fund.  Each of the Filing Persons disclaims beneficial ownership of the shares except to the extent of his or its pecuniary interest therein.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Matthew S. McIlwain</signatureName>
        <signatureDate>2006-12-12</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Matthew S. McIlwain</signatureName>
        <signatureDate>2006-12-12</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Matthew S. McIlwain</signatureName>
        <signatureDate>2006-12-12</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Matthew S. McIlwain</signatureName>
        <signatureDate>2006-12-12</signatureDate>
    </ownerSignature>
</ownershipDocument>
