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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2019-09-11</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001770787</issuerCik>
        <issuerName>10x Genomics, Inc.</issuerName>
        <issuerTradingSymbol>TXG</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001786720</rptOwnerCik>
            <rptOwnerName>Saxonov Serge</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O 10X GENOMICS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>6230 STONERIDGE MALL ROAD</rptOwnerStreet2>
            <rptOwnerCity>PLEASANTON</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94588</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Chief Executive Officer</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Class B Common Stock</value>
                <footnoteId id="F1"/>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>915185</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Series A-1 Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F2"/>
                <footnoteId id="F3"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F2"/>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F2"/>
                <footnoteId id="F3"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class A Common Stock</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>31865</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Class A Common Stock</value>
                <footnoteId id="F4"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F4"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F4"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class B Common Stock</value>
                    <footnoteId id="F4"/>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1250000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Class A Common Stock</value>
                <footnoteId id="F4"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F4"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F4"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class B Common Stock</value>
                    <footnoteId id="F4"/>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1750000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.07</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F6"/>
            </exerciseDate>
            <expirationDate>
                <value>2026-11-18</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class B Common Stock</value>
                    <footnoteId id="F1"/>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>45834</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.20</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F7"/>
            </exerciseDate>
            <expirationDate>
                <value>2027-10-18</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class B Common Stock</value>
                    <footnoteId id="F1"/>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>150000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.20</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F8"/>
            </exerciseDate>
            <expirationDate>
                <value>2027-10-18</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class B Common Stock</value>
                    <footnoteId id="F1"/>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>116667</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>5.04</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F9"/>
            </exerciseDate>
            <expirationDate>
                <value>2028-11-02</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class B Common Stock</value>
                    <footnoteId id="F1"/>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>187500</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>11.48</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F10"/>
            </exerciseDate>
            <expirationDate>
                <value>2029-05-10</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class B Common Stock</value>
                    <footnoteId id="F1"/>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>130600</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Each share of Class B Common Stock shall be reclassified into one share of Class A Common Stock immediately prior to the completion of the Issuer's initial public offering of Class A Common Stock.</footnote>
        <footnote id="F2">Each share of Series A-1 Preferred Stock is convertible into shares of Class A Common Stock at any time at the option of the Reporting Person and automatically upon the occurrence of certain other events set forth in the Issuer's Seventh Amended and Restated Certificate of Incorporation on a one-for-one basis and has no expiration date.  Each share of Class A Common Stock is convertible at any time at the option of the Reporting Person into one share of Class B Common Stock and has no expiration date.  Additionally, each share of Class A Common Stock will convert automatically into one share of Class B Common Stock upon transfer, whether or not for value (subject to certain exceptions) and upon the occurrence of certain other events set forth in the Issuer's Seventh Amended and Restated Certificate of Incorporation.</footnote>
        <footnote id="F3">(Continued from Footnote 2) Each share of Class A Common Stock shall be reclassified into one share of Class B Common Stock and each share of Class B Common Stock shall be reclassified into one share of Class A Common Stock immediately prior to the completion of the Issuer's initial public offering of Class A Common Stock.   As a result of this reclassification, each share of Series A-1 Preferred Stock shall automatically convert into Class B Common Stock on a one-for-one basis immediately prior to the completion of the Issuer's initial public offering of Class A Common Stock.</footnote>
        <footnote id="F4">Each share of Class A Common Stock is convertible at any time at the option of the Reporting Person into one share of Class B Common Stock and has no expiration date.  Additionally, each share of Class A Common Stock will convert automatically into one share of Class B Common Stock upon transfer, whether or not for value (subject to certain exceptions) and upon the occurrence of certain other events set forth in the Issuer's Seventh Amended and Restated Certificate of Incorporation.  Each share of Class A Common Stock shall be reclassified into one share of Class B Common Stock and each share of Class B Common Stock shall be reclassified into one share of Class A Common Stock immediately prior to the completion of the Issuer's initial public offering of Class A Common Stock.</footnote>
        <footnote id="F5">250,000 shares are held by each of Polaris 2018 Irrevocable Trust, Antares 2018 Irrevocable Trust, Arcturus 2018 Irrevocable Trust, FLY 2018 Irrevocable Trust, LY 2018 Irrevocable Trust, MS 2018 Irrevocable Trust and NS 2018 Irrevocable Trust, of which the Reporting Person is the sole trustee.</footnote>
        <footnote id="F6">This option, originally for 200,000 shares, of which 154,166 have been exercised, vested as to one-fourth of the shares on August 1, 2017, and one forty-eighth of the shares subject to the option vest each month thereafter, subject to the Reporting Person continuing as a service provider through each such date.</footnote>
        <footnote id="F7">This option, originally for 300,000 shares, of which 150,000 have been exercised, vested as to one forty-eighth of the shares on October 1, 2017, and one-forty-eighth of the subject to the option vest each month thereafter, subject to the Reporting Person continuing as a service provider through each such date.</footnote>
        <footnote id="F8">This option, originally for 150,000 shares, of which 33,333 have been exercised, vested as to one thirty-sixth of the shares on January 1, 2019, and one thirty-sixth of the subject to the option vest each month thereafter, subject to the Reporting Person continuing as a service provider through each such date.</footnote>
        <footnote id="F9">This option, originally for 250,000 shares, of which 62,500 have been exercised, vested as to one forty-eighth of the shares on October 1, 2018, and one-forty-eighth of the subject to the option vest each month thereafter, subject to the Reporting Person continuing as a service provider through each such date.</footnote>
        <footnote id="F10">This option, originally for 145,786 shares, of which 15,186 have been exercised, vested as to one forty-eighth of the shares on May 1, 2019, and one-forty-eighth of the subject to the option vest each month thereafter, subject to the Reporting Person continuing as a service provider through each such date.</footnote>
    </footnotes>

    <remarks>Exhibit 24 - Power of Attorney</remarks>

    <ownerSignature>
        <signatureName>/s/ Eric S. Whitaker, as Attorney-in-Fact</signatureName>
        <signatureDate>2019-09-11</signatureDate>
    </ownerSignature>
</ownershipDocument>
