UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 14A

Proxy Statement Pursuant to Section 14(a) of

the Securities Exchange Act of 1934

Filed by the Registrant  x                            Filed by a Party other than the Registrant  ¨

Check the appropriate box:

		Illumina, Inc.
		5200 Illumina Way
		San Diego, CA 92122
		tel 858.202.4500
		fax 858.202.4545
		www.illumina.com

Dear Fellow Shareholders –

Our upcoming annual meeting of shareholders is on May 29, 2013. I am writing to ask you to vote FOR Proposal 4 in our proxy statement. With Proposal 4, we are asking that you approve an amendment to our 2005 Stock and Incentive Plan to authorize an additional 5,000,000 shares and extend the term of the plan to June 28, 2016.

The ability to award equity is a fundamental component of our compensation philosophy and an essential element of our total rewards strategy. We strongly believe that this critical tool influences our ability to attract, motivate, and retain talented, key employees thereby influencing our ability to deliver superior shareholder value. We also believe equity is an essential tool to align employee and stockholder interests, link employee compensation with company performance, and maintain a culture based on employee stock ownership. Further, Illumina carefully considers the balance between achieving these objectives and minimizing shareholder dilution before issuing equity to employees.

Illumina’s Board of Directors recommends voting for Proposal 4 to amend the 2005 Stock and Incentive Plan. The attached presentation outlines why we believe Proposal 4 is in the best interest of stockholders and Illumina. Thank you for your attention and consideration in supporting us on this important matter.

Sincerely,

Jay Flatley

Illumina 2013 Proxy Roadshow May 16 - 17, 2013 © 2013 Illumina, Inc. All rights reserved. Illumina, IlluminaDx, BaseSpace, BeadArray, BeadXpress, cBot, CSPro, DASL, DesignStudio, Eco, GAIIx, Genetic Energy, Genome Analyzer, GenomeStudio, GoldenGate, HiScan, HiSeq, Infinium, iSelect, MiSeq, Nextera, NuPCR, SeqMonitor, Solexa, TruSeq, TruSight, VeraCode, the pumpkin orange color, and the Genetic Energy streaming bases design are trademarks or registered trademarks of Illumina, Inc. All other brands and names contained herein are the property of their respective owners.

Safe Harbor Statement 2  This communication may contain statements that are forward-looking.  Forward-looking statements are subject to known and unknown risks and uncertainties and are based on potentially inaccurate assumptions that could cause actual results to differ materially from those expected or implied by the forward-looking statements.  Among the important factors that could cause actual results to differ materially from those in any forward-looking statements are (i) our ability to develop and commercialize further our sequencing, array, PCR, diagnostics, and consumables technologies and to deploy new products and applications, and expand the markets, for our technology platforms, (ii) our ability to manufacture robust instrumentation and consumables, (iii) significant uncertainty concerning government and academic research funding worldwide as governments in the United States and Europe, in particular, focus on reducing fiscal deficits while at the same time confronting slowing economic growth, and (iv) other factors detailed in our filings with the U.S. Securities and Exchange Commission (“SEC”), including our most recent filings on Forms 10-K and 10- Q, or in information disclosed in public conference calls, the date and time of which are released beforehand.  Illumina undertakes no obligation, and does not intend, to update these forward-looking statements.

Requests an amendment to our 2005 Stock and Incentive Plan: Illumina’s Board of Directors Recommends a Yes Vote: Illumina Investor Presentation Executive Summary of Proposal 4 We must attract, retain, and motivate high-performers in order to generate long-term shareholder value We use equity compensation to align employee and shareholder interests We have a disciplined annual share granting practice to limit dilution We proactively manage our outstanding shares through equity repurchases Authorize an additional 5 million shares to the plan Extend the term of the Plan to June 28, 2016 Additional shares are expected to last three years 3

2012 Revenue of $1.15 billion Guidance of 15% revenue growth in 2013  Over 2,400 employees globally; headquartered in San Diego, CA Recognized leader in next-generation sequencing >90% of the world’s sequencing data generated using Illumina platforms Recognized leader in microarrays with ~80% market share in DNA genotyping Strong diagnostic effort in reproductive health and cancer Unmatched history of innovation and strong R&D pipeline Who is Illumina? Worldwide Leader in Genomic Analysis         1.  Revenue guidance given via press release and 8-K on January 28, 2013; guidance was not reaffirmed or updated post Q1’13 financial results 4 1

Illumina’s Markets 2013 Over $12 Billion Opportunity  Improve human health by unlocking the power of the genome Consumer Markets Life Science Research ~$4B Applied Markets ~$1B Clinical & Translational ~$6B Reproductive Health ~$1B >$50M 5

Illumina’s Equity Compensation Philosophy Program is Based on Guiding Principles Equity Compensation: Used to attract, retain and motivate new and existing employees Aligns employee and stockholder interests Granted to our highest performing employees and senior executives to generate long-term shareholder value 6

7 Share Balance by Year 5 Million Shares Will Fund Program for 3 Years Available Shares to Grant (M) Evergreen expired in 2010 0 2,500 5,000 2008 2009 2010 2011 2012 7,500

Net Grants by Year Net Grant Levels Have Been Stable While the Number of Employees has Grown       2,500 2,000 1,500 1,000 500 0 2008 2009 2010 2011 2012 Net Grants (M) Employees 8

9 Gross Burn Rate Disciplined Annual Share Granting Practice Our net burn rate averaged ~3.0% over the last five years Gross Burn Rate (%) 4.8% 3.4% 3.8% 4.0% 3.4% 1.5% 3.0% 4.5% 2008 2009 2010 2011 2012 0.0%

Outstanding Options Employee Interests are Closely Aligned with Non-Employee Shareholders         Employees are holding more than 6 million in the money options at a weighted average price of $24.49 Outstanding Options by Expiry Date Outstanding Options by Strike Price 1. Includes options being held by the Board of Directors as of December 30, 2012 2. Includes options granted under the 2005 Stock and Incentive Plan, New Hire Stock and Incentive Plan, and the Solexa plan 1,200 1,000 800 600 400 200 - $5 $10 $15 $20 $25 $30 $35 $40 $45 $50 $55 $60 $65 $70 $75 $80 Exercisable Unvested - 200 400 600 800 1,000 1,200 1,400 1,600 1,800 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 Exercisable Unvested 10 1

Repurchased  Shares (M) Capital Deployment Strategy for Long-Term Growth Equity Buybacks Partially Offset Dilution from Shares Granted   Equity Repurchases $250 million authorization; ~$140 million remaining Committed to returning cash to shareholders Expanded sales force Infrastructure investments; ERP and customer supply improvement programs Clinical and diagnostic infrastructure Invest for Growth Technology and Diagnostic Acquisitions BlueGnome:  IVF, Cancer and Cytogenetics Verinata Health:  Non-invasive Prenatal Testing 1. Repurchased shares exclude 4.9 million shares repurchased in tandem with the issuance of the 2016 convertible bond 1 6 4 2 0 3.1 6.1 0.8 4.3 1.9 2008 2009 2010 2011 2012 11

12 Leading Talent Brings Superior Revenue & EPS Growth 2013 Guidance is for 15% Revenue Growth¹ Revenue CAGR: 19% EPS CAGR : 24% 1.  Revenue guidance given via press release and 8-K on January 28, 2013; guidance was not reaffirmed or updated post Q1’13 financial results 2.  Non-GAAP Diluted EPS $0.00 $0.40 $0.80 $1.20 $1.60 $400 $800 $1,200 2008 2009 2010 2011 2012 Revenue ($M) non -GAAP EPS $0 2

13 Five-Year Stock Performance Compensation Philosophy and Execution Delivers Superior Shareholder Value  HiSeq 2000 and Genome Analyzer IIe Launched HiScanSQ Begins Shipping iScan Launched Eco Real-Time  PCR System Launched Epicentre Acquisition MiSeq & BaseSpace Launched HiSeq 2500 Announced 0% 50% 100% 150% 200% 250% 300% ILMN S&P 500 Life Sciences 188% 109% 121% 1. Stock performance as defined by total return to shareholders 2. Life Sciences return is an average of total shareholder return of A, AFFX, BRKR, DHR, HOLX, LIFE, PKI, QGEN, SIAL, TECH, TMO and WAT

14 Financial Guidance Financial Outlook Illumina Will Continue to Deliver Strong Growth for the Foreseeable Future 2013 Revenue: 15% YoY Growth Gross Margin: ~ 70% Non-GAAP EPS : $1.55 - $1.62 ETR%: 31% Stock Based Compensation Expense: $115M Shares Outstanding: ~134M 1.  Revenue guidance given via press release and 8-K on January 28, 2013; guidance was not reaffirmed or updated post Q1’13 financial results 2.  Non-GAAP EPS guidance includes stock based compensation Future Growth Drivers 2014 and Beyond Key Target Markets: – Clinical & Translational: $6B – Life sciences: $4B – Reproductive Health: $1B – Applied markets: $1B – Consumer:  $50M Reproductive Health Diagnostics:  – 1.2 – 1.5M IVF cycles annually  – 500 – 750K high risk pregnancies in the U.S. alone – Carrier screening, CF assay and MiSeq DX platform 2 1

Illumina’s Board of Directors  Recommends a Yes Vote on Proposal 4 Conclusion 15 We use equity compensation to align employee and shareholder interests We have a disciplined annual share granting practice We have a strong track record of performance stemming from our overall strategic plan, including equity compensation We have a robust equity repurchase plan and intend to continue repurchases over the life of our 2005 Stock and Incentive Plan

16