Prospectus Supplement No. 1

Filed Pursuant to
Rule 424(b)(3) and (c)
File No. 333-127460

13,657,101 Shares of Common Stock

SOLEXA, INC.

     This prospectus supplement supplements the prospectus, dated September 1, 2005, of Solexa, Inc. relating to the offering and sale by selling stockholders of Solexa (or by donees, pledgees, transferees and other successors in interest that receive such shares as a gift, pledge, partnership distribution or other non-sale transfer) of up to 13,657,101 shares of our common stock. This prospectus supplement should be read in conjunction with the prospectus, and is qualified by reference to the prospectus, except to the extent that the information presented herein supercedes the information contained in the prospectus. The term “Selling Stockholders” as used in the prospectus shall be deemed to include the selling stockholders identified in the table below. This prospectus supplement is not complete without, and may not be delivered or utilized except in connection with, the prospectus, including any amendments or supplements thereto.

     Investing in our common stock involves a high degree of risk. See “Risk Factors” beginning on page 2 of the prospectus.

     NEITHER THE SECURITIES AND EXCHANGE COMMISSION NOR ANY STATE SECURITIES COMMISSION HAS APPROVED OR DISAPPROVED OF THESE SECURITIES OR PASSED UPON THE ADEQUACY OR ACCURACY OF THIS PROSPECTUS. ANY REPRESENTATION TO THE CONTRARY IS A CRIMINAL OFFENSE.

The date of this prospectus is January 19, 2006.

     This prospectus supplement is being filed in connection with the distribution of shares held by Oxford BioScience Partners IV L.P. and mRNA Fund II L.P., together the Oxford Funds, each identified in the prospectus as selling stockholders, to their respective partners. No additional shares of Solexa common stock are being offered for resale hereunder. Except with respect to directors and officers of Solexa, the entities that have filed reports pursuant to Section 13(f) of the Securities Exchange Act of 1934, as amended, or the Act, and statements of beneficial ownership filed pursuant to Sections 13(d) and 13(g) of the Act, the ownership indicated in the table below is based solely on shares owned by the indicated selling stockholders as a result of a distribution of shares by the Oxford Funds on January 18, 2006. The table appearing on pages 10-13 of the prospectus under the caption “Selling Stockholders” is supplemented and amended to include the following stockholders in addition to those identified in the prospectus:

Shares of Common

Shares of Common

Stock Beneficially

Number

Stock Beneficially

Owned Prior to the

of

Owned After

Offering

Shares

Offering

Being

Security Holders***

Shares

Percent*

Offered

Shares

Percent*

Oxford BioScience Partners IV L.P. (1), (2)

1,035,610

3.44

%

490,819

544,791

1.81

%

mRNA Fund II L.P. (1), (3)

10,388

*

*

5,104

5,284

*

*

125 Broad Street Fund, LLC

6,534

*

*

6,534

0

*

*

AGF IART

13,069

*

*

13,069

0

*

*

AGF VIE

30,494

*

*

30,494

0

*

*

Akzo Nobel Pharma Ventures B.V.

4,356

*

*

4,356

0

*

*

Alexandra R. Pearsall

26

*

*

26

0

*

*

Alison Taunton-Rigby

218

*

*

218

0

*

*

ALPHA 2001 L.P.

10,891

*

*

10,891

0

*

*

American Family Mutual Insurance Company

30,494

*

*

30,494

0

*

*

Artal Invest Ltd.

43,563

*

*

43,563

0

*

*

Ashley J. Stevens

436

*

*

436

0

*

*

Barry I. Eisenstein

436

*

*

436

0

*

*

Bear Stearns Private Equity Limited

10,891

*

*

10,891

0

*

*

Bernd R. Seizinger

436

*

*

436

0

*

*

Big Woods II LLC

21,781

*

*

21,781

0

*

*

Brent B. Milner

218

*

*

218

0

*

*

California Emerging Ventures II LLC

130,689

*

*

130,689

0

*

*

Catherine M. Stone Rev Tr dtd 10/18/99

1,089

*

*

1,089

0

*

*

Chaos Partners I, L.P.

4,356

*

*

4,356

0

*

*

Charles Schwab & Co., FBO Richard S. Foemmel IRA Account

436

*

*

436

0

*

*

Christopher Covington

436

*

*

436

0

*

*

Cornelius T. Ryan

108

*

*

108

0

*

*

Credit Suisse Anlagestiftung

6,534

*

*

6,534

0

*

*

CTTV Investments LLC

8,713

*

*

8,713

0

*

*

David J. Livingston, Trustee of the David J. Livingston Rev Trust — 2002

218

*

*

218

0

*

*

Dennis H. and Susan F. Langer

218

*

*

218

0

*

*

Dogwood Investments, Inc.

21,781

*

*

21,781

0

*

*

Shares of Common

Shares of Common

Stock Beneficially

Number

Stock Beneficially

Owned Prior to the

of

Owned After

Offering

Shares

Offering

Being

Security Holders***

Shares

Percent*

Offered

Shares

Percent*

Donald E. and Janet L. Schoeny

436

*

*

436

0

*

*

Dr. Jules and Mrs. Barbara Blake

108

*

*

108

0

*

*

Dr. Stephen Ashley Lawton & Mrs. Alison Frances Lawton

218

*

*

218

0

*

*

Edward B. Roberts

436

*

*

436

0

*

*

Edward R. Gates

326

*

*

326

0

*

*

Eric W. Roberts

436

*

*

436

0

*

*

Fire and Police Pension Association of Colorado

21,781

*

*

21,781

0

*

*

Fort Washington Private Equity Investors III, L.P.

43,563

*

*

43,563

0

*

*

Frederick Frank

218

*

*

218

0

*

*

GE Capital Equity Holdings, Inc.

65,344

*

*

65,344

0

*

*

General Practitioner LLC

2,396

*

*

2,396

0

*

*

Genzyme Corporation

21,781

*

*

21,781

0

*

*

Georges Haas

218

*

*

218

0

*

*

GIMV NV — London Branch

52,276

*

*

52,276

0

*

*

Godfrey S. Rockefeller “C” Tr dtd 12/12/63 FBO Marion R. Stone

1,089

*

*

1,089

0

*

*

Gordon M. Binder and Adele H. Binder, trustees of the Binder Trust dated July 15, 2003

13,069

*

*

13,069

0

*

*

GS PEP 1999 Manager Fund Technology Holdings, LLC

1,551

*

*

1,551

0

*

*

GS PEP Technology Fund 2000 Offshore Holdings, L.P.

19,277

*

*

19,277

0

*

*

GS PEP Technology Fund 2000, L.P.

48,847

*

*

48,847

0

*

*

GS Private Equity Partners 2000 — Manager Fund, L.P.

18,993

*

*

18,993

0

*

*

GS Private Equity Partners 2000 Offshore Holdings, L.P.

17,207

*

*

17,207

0

*

*

GS Private Equity Partners 2000, L.P.

50,925

*

*

50,925

0

*

*

HarbourVest Partners VI-Parallel Partnership Fund L.P.

3,267

*

*

40,296

0

*

*

HarbourVest Partners VI-Partnership Fund L.P.

40,296

*

*

3,267

0

*

*

HarbourVest VII Venture Ltd.

21,781

*

*

21,781

0

*

*

Health Advances, Inc.

436

*

*

436

0

*

*

Helen S. Fitzgerald

436

*

*

436

0

*

*

Henry E. Blair

218

*

*

218

0

*

*

HFI Private Equity, Ltd.

32,672

*

*

32,672

0

*

*

Hiorts Finance SA

8,713

*

*

8,713

0

*

*

Shares of Common

Shares of Common

Stock Beneficially

Number

Stock Beneficially

Owned Prior to the

of

Owned After

Offering

Shares

Offering

Being

Security Holders***

Shares

Percent*

Offered

Shares

Percent*

Howard Hughes Medical Institute

87,127

*

*

87,127

0

*

*

Immunex Corporation

8,713

*

*

8,713

0

*

*

International Business Machines Corporation

21,781

*

*

21,781

0

*

*

Jack H. Morgan

218

*

*

218

0

*

*

Jean Montagu

436

*

*

436

0

*

*

Jeffrey A. Leerink

326

*

*

326

0

*

*

Jeffrey Matthews

436

*

*

436

0

*

*

Jennifer P. Stone 1991 Revocable Trust

1,089

*

*

1,089

0

*

*

Joel S. Marcus

436

*

*

436

0

*

*

John J. & Wendy G. J. Troy

436

*

*

436

0

*

*

John R. Brown

326

*

*

326

0

*

*

Joseph R. Hyde, III

43,563

*

*

43,563

0

*

*

JP Morgan Bank, trustee for the BP Master Trust for Employee Pension Plans

43,563

*

*

43,563

0

*

*

JPMorgan Chase Retirement Plan

21,781

*

*

21,781

0

*

*

Justin P. Morreale

436

*

*

436

0

*

*

Karl H. Proppe

218

*

*

218

0

*

*

Kenneth A. Sorensen

436

*

*

436

0

*

*

Kenneth Ward

218

*

*

218

0

*

*

Klee USA Fund I, L.P.

32,672

*

*

32,672

0

*

*

Larry Abrams

436

*

*

436

0

*

*

Lee Brettman

436

*

*

436

0

*

*

Los Angeles County Employees Retirement Association

87,127

*

*

87,127

0

*

*

Lucy S. Moore

1,089

*

*

1,089

0

*

*

Luna PCC Limited 2000 Cell

436

*

*

436

0

*

*

Marc Kozin

326

*

*

326

0

*

*

Margraf Investments, LLC

436

*

*

436

0

*

*

Marion R. Stone

1,089

*

*

1,089

0

*

*

Marion R. Stone Tr dtd 12/30/87

2,178

*

*

2,178

0

*

*

Markaz Offshore Direct Investments

4,356

*

*

4,356

0

*

*

Matthew L. Clark

108

*

*

108

0

*

*

MC Life Science Ventures, Inc.

13,069

*

*

13,069

0

*

*

MCC-PCG International Private Equity Fund

13,069

*

*

13,069

0

*

*

Mellon Trust of New England, N.A., f/k/a Boston Safe Deposit and Trust Company as Trustee for the Qwest Occupational Health Trust

9,802

*

*

9,802

0

*

*

Mellon Trust of New England, N.A., f/k/a Boston Safe Deposit and Trust Company as Trustee for the Qwest Pension Trust

55,543

*

*

55,543

0

*

*

Shares of Common

Shares of Common

Stock Beneficially

Number

Stock Beneficially

Owned Prior to the

of

Owned After

Offering

Shares

Offering

Being

Security Holders***

Shares

Percent*

Offered

Shares

Percent*

Mellon Trust of New England, N.A., f/k/a Boston Safe Deposit and Trust Company, as Trustee for the Raytheon Master Pension Trust

87,127

*

*

87,127

0

*

*

Michael E. Lytton

53

*

*

53

0

*

*

Michael R. Pavia

436

*

*

436

0

*

*

Nationwide Mutual Insurance Company

21,781

*

*

21,781

0

*

*

Nippon Life Insurance Company

43,563

*

*

43,563

0

*

*

Nordea Thematic Fund of Funds I k/s

8,713

*

*

8,713

0

*

*

OBP Management IV L.P. (1), (4)

19,998

*

*

19,998

0

*

*

Palladian Partners 2001, LLC

10,891

*

*

10,891

0

*

*

Palmer & Dodge LLP

218

*

*

218

0

*

*

Partners Group Private Equity Performance Holding Limited

17,425

*

*

17,425

0

*

*

Paul A. Kirkconnell

436

*

*

436

0

*

*

Pearl Holding Limited

21,781

*

*

21,781

0

*

*

Peter Lanciano

436

*

*

436

0

*

*

Peter O. Kliem & Ann Wolff

218

*

*

218

0

*

*

Peter Preuss

2,178

*

*

2,178

0

*

*

Peter Wirth

436

*

*

436

0

*

*

Philip J. Edmundson

326

*

*

326

0

*

*

Philip V. Holberton

218

*

*

218

0

*

*

Pravin R. Chaturvedi

326

*

*

326

0

*

*

Private Equity Investment Fund IV, LP

13,069

*

*

13,069

0

*

*

Private Equity Technology Partners III C.V.

43,563

*

*

43,563

0

*

*

Raymond N. Charest

26

*

*

26

0

*

*

RGIP, LLC

436

*

*

436

0

*

*

Rho Fund Investors II LLC

21,781

*

*

21,781

0

*

*

Richard H. Egdahl

218

*

*

218

0

*

*

Robert E. Flaherty

218

*

*

218

0

*

*

Robert Granovsky

218

*

*

218

0

*

*

Robert J. Hennessey

436

*

*

436

0

*

*

Scott M. Rocklage

436

*

*

436

0

*

*

Shalon Ventures L.P.

436

*

*

436

0

*

*

Silicon Valley Bancshares

2,178

*

*

2,178

0

*

*

Stone Street PEP Technology Fund 2000, L.P.

17,451

*

*

17,451

0

*

*

Suzanne Troy Cole

436

*

*

436

0

*

*

Teachers Insurance and Annuity Association of America

87,127

*

*

87,127

0

*

*

TH&T Partners 2001, LLC

436

*

*

436

0

*

*

The Bear Stearns Companies, Inc.

10,891

*

*

10,891

0

*

*

Shares of Common

Shares of Common

Stock Beneficially

Number

Stock Beneficially

Owned Prior to the

of

Owned After

Offering

Shares

Offering

Being

Security Holders***

Shares

Percent*

Offered

Shares

Percent*

The John T. Lupton Trust

10,891

*

*

10,891

0

*

*

The Lloyd Cotsen 1985 Trust

10,891

*

*

10,891

0

*

*

The Markaz/Hamilton Lane Technology Fund L.P.

13,069

*

*

13,069

0

*

*

The Norinchukin Bank

21,781

*

*

21,781

0

*

*

The Regents of the University of California

108,907

*

*

108,907

0

*

*

The Robert and Francine Lent Living Trust

10,891

*

*

10,891

0

*

*

Timothy B. Stone 1994 Rev Tr

436

*

*

436

0

*

*

Timothy R. Surgenor

218

*

*

218

0

*

*

Tri-State Growth Capital Fund I L.P.

21,781

*

*

21,781

0

*

*

Trustees of Boston University

8,713

*

*

8,713

0

*

*

United of Omaha Life Insurance Company

21,781

*

*

21,781

0

*

*

Victor W. Schmitt

326

*

*

326

0

*

*

Vincent P. Stanton, Jr.

173

*

*

173

0

*

*

V-Sciences Fund Investments Pte Ltd

21,781

*

*

21,781

0

*

*

Wachovia Investors, Inc.

21,781

*

*

21,781

0

*

*

William A. Holodnak

218

*

*

218

0

*

*

Subtotal

3,045,998

10.54

%

2,495,923

550,075

1.83

%

*		Percentage calculations based on 30,097,987 shares of our common stock that were issued and outstanding as of January 18, 2006.
**		Represents beneficial ownership of less than 1%.
***		Addresses that are not listed are c/o Oxford BioScience Partners VI L.P., 222 Berkeley Street, Boston, MA 02116.
(1)		OBP Management IV L.P. is the general partner for Oxford Bioscience Partners IV L.P. and mRNA Fund II L.P. Mark Carthy, a former director of Solexa, is a General Partner of OBP Management IV L.P. and may be deemed to share voting and investment power over the shares held by Oxford Bioscience Partners IV L.P. and mRNA Fund II L.P. Mr. Carthy disclaims beneficial ownership of such shares except to the extent of his pecuniary interest therein. Doug Fambrough, a director of Solexa, is affiliated with Oxford Bioscience Partners IV, L.P. and mRNA Fund II L.P. and does not possess voting and/or investment power of the shares held by these entities. Dr. Fambrough disclaims beneficial ownership of such shares except to the extent of his pecuniary interest therein. Excludes 1,559 shares of restricted common stock and options to purchase 20,000 shares of common stock held by Dr. Fambrough.
(2)		Includes 272,268 shares of common stock issuable upon exercise of a warrant.
(3)		Includes 2,732 shares of common stock issuable upon exercise of a warrant.
(4)		Excludes 763,342 shares of common stock held by Oxford BioScience Partners IV L.P., 272,268 shares of common stock issuable upon exercise of a warrant held by Oxford BioScience Partners IV L.P., 27,523 shares of common stock held by mRNA Fund II L.P. and 2,732 shares of common stock issuable upon exercise of a warrants held by mRNA Fund II L.P.