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

    <schemaVersion>X0303</schemaVersion>

    <documentType>4/A</documentType>

    <periodOfReport>2009-04-28</periodOfReport>

    <dateOfOriginalSubmission>2009-04-30</dateOfOriginalSubmission>

    <notSubjectToSection16>false</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001217007</rptOwnerCik>
            <rptOwnerName>JURGENSEN ELLIOTT REN JR</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>2644 W. LK. SAMM. PKWY. NE</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>REDMOND</rptOwnerCity>
            <rptOwnerState>WA</rptOwnerState>
            <rptOwnerZipCode>98052</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>true</isDirector>
            <isOfficer>false</isOfficer>
            <isTenPercentOwner>false</isTenPercentOwner>
            <isOther>false</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2009-04-28</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>false</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>20000</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>2.5588</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>20000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">The amount and price reported in this Column 4 reflect the aggregate number and weighted-average purchase price, respectively, of the securities acquired. These shares were purchased in multiple transactions at prices ranging from $2.54 to $2.61, inclusive.  For all transactions reported in this Form 4 utilizing a weighted-average price, the reporting person undertakes to provide to the issuer, any security holder of the issuer, or the SEC staff, upon request, information regarding the number of shares sold at each price within the range.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>Keenan M. Conder, Attorney-in-Fact</signatureName>
        <signatureDate>2009-05-19</signatureDate>
    </ownerSignature>
</ownershipDocument>
