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

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2009-02-19</periodOfReport>

    <notSubjectToSection16>false</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001381752</rptOwnerCik>
            <rptOwnerName>McIlwain Matthew S</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O MADRONA VENTURE GROUP, LLC</rptOwnerStreet1>
            <rptOwnerStreet2>1000 SECOND AVE., STE. 3700</rptOwnerStreet2>
            <rptOwnerCity>SEATTLE</rptOwnerCity>
            <rptOwnerState>WA</rptOwnerState>
            <rptOwnerZipCode>98104</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>true</isDirector>
            <isOfficer>false</isOfficer>
            <isTenPercentOwner>true</isTenPercentOwner>
            <isOther>false</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>8509117</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F1"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2009-02-19</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>false</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>11150</value>
                    <footnoteId id="F2"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>2.269</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>31750</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Represents (a) 6,860,834 shares of common stock held by MadronaVenture Fund I-A, LP; (b) 746,721 shares of common stock held by Madrona Venture Fund I-B, LP; and (c) 901,562 shares of common stock held by Madrona Managing Director Fund LLC. Mr. McIlwain is a managing director and member of various entities affiliated with Madrona Venture Group, LLC. Mr. McIlwain does not have sole voting or dispositive authority over these shares and disclaims beneficial ownership of these shares except to the extent of his pecuniary interest therein.</footnote>
        <footnote id="F2">The &quot;Amount&quot; and &quot;Price&quot; disclosed in this Column 4 reflect the aggregate amount of securities and the average purchase price (ranging from $2.25 to $2.30 per share) in connection with the following purchases:  6,450 shares at $2.25; 400 shares at $2.26; 200 shares at $2.27; and 4,100 shares at $2.30.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>Keenan Conder, Attorney-in-Fact</signatureName>
        <signatureDate>2009-02-20</signatureDate>
    </ownerSignature>
</ownershipDocument>
