AN DIEGO — Illumina, Inc. (NASDAQ:ILMN) today announced its financial results for the first quarter of 2013.

First quarter 2013 results:

Revenue of $331 million, a 21% increase compared to $273 million in the first quarter of 2012

GAAP net loss for the quarter of $23 million, or $0.18 per diluted share due to a charge of $106.9 million related to the Syntrix Biosystems, Inc.

litigation; this compared to net income of $26 million, or $0.20 per diluted share, for the first quarter of 2012

Non-GAAP net income for the quarter of $63 million, or $0.46 per diluted share, compared to non-GAAP net income of $48 million, or $0.36 per diluted share, for the first quarter of 2012 (see the table entitled “Itemized Reconciliation Between GAAP and Non-GAAP Net Income (Loss)” for a reconciliation of these GAAP and non-GAAP financial measures)

Cash flow from operations of $88 million and free cash flow of $66 million for the quarter

Gross margin in the first quarter of 2013 was 66.3% compared to 66.4% in the prior year period. Excluding the effect of non-cash charges associated with stock compensation, amortization of acquired intangible assets, amortization of inventory revaluation costs and legal contingencies, non-GAAP gross margin was 69.2% for the first quarter of 2013 compared to 69.0% in the prior year period.

Research and development (R&D) expenses for the first quarter of 2013 were $61.5 million compared to $48.8 million in the first quarter of 2012. R&D expenses included $8.0 million and $7.4 million of non-cash stock compensation expense in the first quarters of 2013 and 2012, respectively. Excluding these charges and contingent compensation expense, R&D expenses as a percentage of revenue were 16.0% compared to 14.9% in the prior year period.

Selling, general and administrative (SG&A) expenses for the first quarter of 2013 were $85.1 million compared to $68.0 million for the first quarter of 2012. SG&A expenses included $14.6 million and $13.8 million of non-cash stock compensation expense in the first quarters of 2013 and 2012, respectively. Excluding these charges, contingent compensation expense, and amortization of acquired intangible assets, SG&A expenses as a percentage of revenue were 19.9% compared to 18.9% in the prior year period.

Legal contingency expenses for the first quarter of 2013 were $106.9 million as a result of a jury decision, announced on March 14, 2013, in the patent litigation brought by Syntrix Biosystems, Inc. Legal contingency expenses were $2.2 million in the first quarter of 2012. Illumina continues to believe that Syntrix’s claims are without merit and intends to file post-trial motions asking the court to vacate the jury’s finding and to rule as a matter of law that the BeadChip does not infringe Syntrix’s patent.

Depreciation and amortization expenses were $20.5 million and capital expenditures were $21.4 million during the first quarter of 2013. The Company ended the quarter with $1.07 billion in cash, cash equivalents and short-term investments, compared to $1.35 billion as of December 30, 2012.

“We are pleased with our first quarter results,” said Illumina’s President and Chief Executive Officer Jay Flatley. “Our business demonstrated strong growth across the entire portfolio, which resulted in record revenue, and we made significant progress on furthering our reproductive health strategy with the closing of the Verinata acquisition. We are now focused on continuing to deliver on our 2013 strategic initiatives for strong long-term growth.”

Updates since our last earnings release:

Completed the acquisition of Verinata Health, Inc., a leading provider of non-invasive tests for the early identification of fetal chromosomal abnormalities

Announced an unfavorable jury finding in patent litigation with Syntrix Biosystems, Inc. regarding Illumina’s BeadChip array product

Announced a favorable ruling in patent litigation against Life Technologies

Announced that iCOGS custom array was used to identify genetic variants related to breast, ovarian and prostate cancer as part of the Collaborative Oncological Gene-Environment Study (COGS)

Launched TruSight Tumor content set for NGS-based somatic variant detection in solid tumors

Announced an agreement with Kindstar Global to facilitate adoption of Illumina technologies in Asia

Named Charles Dadswell, formerly bioMerieux’s General Counsel for North and Latin America and Corporate Director of Global Intellectual Property, as General Counsel

Repurchased $25 million of common stock under our previously announced share repurchase program

Quarterly conference call information

The conference call will begin at 2:00 pm Pacific Time (5:00 pm Eastern Time) on Monday, April 22, 2013. Interested parties may listen to the call by dialing 888.679.8033 (passcode: 58226131), or, if outside North America, by dialing +1.617.213.4846 (passcode: 58226131). Individuals may access the live teleconference in the Investor Relations section of Illumina’s web site under the “Company” tab at www.illumina.com.

A replay of the conference call will be available from 4:00 pm Pacific Time (7:00 pm Eastern Time) on April 22, 2013 through April 29, 2013 by dialing 888.286.8010 (passcode: 31374623), or if outside North America, by dialing +1.617.801.6888 (passcode: 31374623).

Statement regarding use of non-GAAP financial measures

The Company reports non-GAAP results for diluted net income per share, net income, gross margins, operating expenses, operating margins, other income (expense), and free cash flow in addition to, and not as a substitute for, or superior to, financial measures calculated in accordance with GAAP.

The Company’s financial measures under GAAP include substantial charges related to legal contingencies, stock compensation expense, non-cash interest expense associated with the Company’s convertible debt instruments that may be settled in cash, amortization expense related to acquired intangible assets, costs related to unsolicited tender offer for the Company’s stock, gains related to cost-method investments, contingent compensation expense, acquisition related expense, headquarter relocation expense, amortization of inventory revaluation costs, and restructuring charges. Per share amounts also include the double dilution associated with the accounting treatment of the Company’s 0.625% convertible senior notes outstanding and the corresponding call option overlay. Management believes that presentation of operating results that excludes these items and per share double dilution provides useful supplemental information to investors and facilitates the analysis of the Company’s core operating results and comparison of operating results across reporting periods. Management also believes that this supplemental non-GAAP information is therefore useful to investors in analyzing and assessing the Company’s past and future operating performance.

The Company encourages investors to carefully consider its results under GAAP, as well as its supplemental non-GAAP information and the reconciliation between these presentations, to more fully understand its business. About Illumina

Illumina (www.illumina.com) is a leading developer, manufacturer, and marketer of life science tools and integrated systems for the analysis of genetic variation and function. We provide innovative sequencing and array-based solutions for genotyping, copy number variation analysis, methylation studies, gene expression profiling, and low-multiplex analysis of DNA, RNA, and protein. We also provide tools and services that are fueling advances in consumer genomics and diagnostics. Our technology and products accelerate genetic analysis research and its applications, paving the way for molecular medicine and ultimately transforming healthcare