Cepheid (CPHD) 10-Q 2009 Q2 Quarterly report

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q

(Mark One)

x QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended June 30, 2009

OR

¨ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from              to             

Commission file number 000-30755

CEPHEID

(Exact Name of Registrant as Specified in its Charter)

California	77-0441625
(State or Other Jurisdiction of Incorporation or Organization)	(I.R.S. Employer Identification No.)
904 Caribbean Drive, Sunnyvale, California	94089-1189
(Address of Principal Executive Office)	(Zip Code)

(408) 541-4191

(Registrant’s Telephone Number, Including Area Code)

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes  x    No  ¨

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    Yes  ¨    No  ¨

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See definitions of “large accelerated filer,” “accelerated filer,” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):

Large Accelerated Filer	x	Accelerated Filer	¨
Non-Accelerated Filer	¨  (Do not check if a smaller reporting company)	Smaller Reporting Company	¨

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).    Yes  ¨    No  x

As of July 24, 2009 there were 58,127,812 shares of the registrant’s common stock outstanding.

REPORT ON FORM 10-Q FOR THE

QUARTER ENDED JUNE 30, 2009

INDEX

		Page
Part I.	Financial Information
Item 1.	Financial Statements	3
	Condensed Consolidated Balance Sheets as of June 30, 2009 and December 31, 2008	3
	Condensed Consolidated Statements of Operations for the three and six months ended June 30, 2009 and 2008	4
	Condensed Consolidated Statements of Cash Flows for the six months ended June 30, 2009 and 2008	5
	Notes to Condensed Consolidated Financial Statements	6
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	22
Item 3.	Quantitative and Qualitative Disclosures About Market Risk	28
Item 4.	Controls and Procedures	29
Part II.	Other Information
Item 1.	Legal Proceedings	30
Item 1A	Risk Factors	30
Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds	39
Item 3.	Defaults Upon Senior Securities	39
Item 4.	Submission of Matters to a Vote of Security Holders	39
Item 5.	Other Information	40
Item 6.	Exhibits	40
Signatures		41

Cepheid^®, the Cepheid logo, GeneXpert^®, Xpert^®, SmartCycler^®, SmartCycler II, SmartCap^®, I-CORE^®, SmartMix^® and OmniMix^®, are trademarks of Cepheid. All other trademarks, service marks or trade names referred to in this report are the property of their respective owners.

PART I — FINANCIAL INFORMATION

ITEM 1. FINANCIAL STATEMENTS

CEPHEID

CONDENSED CONSOLIDATED BALANCE SHEETS

(in thousands, except share data)

	June 30, 2009			December 31, 2008
	(unaudited)			As Restated (1)
ASSETS
Current assets:
Cash and cash equivalents	$	24,726		$	23,478
Restricted cash		—			1,500
Short-term investments		22,004			—
Put option		2,920			—
Accounts receivable, net		20,828			18,952
Inventory		35,251			33,498
Prepaid expenses and other current assets		2,485			4,636
Total current assets		108,214			82,064
Property and equipment, net		22,780			24,109
Investments		—			15,101
Put option		—			9,438
Other non-current assets		493			920
Intangible assets, net		34,235			33,791
Goodwill		18,626			18,556
Total assets	$	184,348		$	183,979
LIABILITIES AND SHAREHOLDERS’ EQUITY
Current liabilities:
Accounts payable	$	12,458		$	9,669
Accrued compensation		8,187			7,919
Accrued royalties		7,122			5,953
Accrued collaboration profit sharing		872			2,023
Accrued and other liabilities		7,495			6,816
Current portion of deferred revenue		2,753			2,834
Bank borrowing		14,598			14,639
Total current liabilities		53,485			49,853
Long-term portion of deferred revenue		1,840			1,753
Other liabilities		4,641			3,549
Total liabilities		59,966			55,155
Commitments and contingencies (Note 8)
Shareholders’ equity:
Preferred stock, no par value; 5,000,000 shares authorized, none issued or outstanding		—			—
Common stock, no par value; 100,000,000 shares authorized, 58,121,360 and 57,663,859 shares issued and outstanding at June 30, 2009 and December 31, 2008, respectively		269,374			266,991
Additional paid-in capital		49,117			41,619
Accumulated other comprehensive income (loss)		35			(23	)
Accumulated deficit		(194,144	)		(179,763	)
Total shareholders’ equity		124,382			128,824
Total liabilities and shareholders’ equity	$	184,348		$	183,979

(1) See Note 11, “Restatement of Condensed Consolidated Financial Statements” in Notes to Condensed Consolidated Financial Statements.

The accompanying notes are an integral part of these Consolidated Financial Statements.

3

CEPHEID

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS

(in thousands, except per share data)

(unaudited)

	Three Months Ended June 30,						Six Months Ended June 30,
	2009			2008			2009			2008
				As Restated (1)						As Restated (1)
Revenues:
System sales	$	8,911		$	12,423		$	16,820		$	26,747
Reagent and disposable sales		30,649			26,530			59,328			54,126
Total product sales		39,560			38,953			76,148			80,873
Other revenue		1,461			3,097			3,640			6,010
Total revenues		41,021			42,050			79,788			86,883
Costs and operating expenses:
Cost of product sales		23,250			23,039			43,940			46,193
Collaboration profit sharing		2,612			2,777			5,241			6,510
Research and development		10,315			10,964			20,653			20,862
Sales and marketing		6,917			7,434			13,729			14,375
General and administrative		5,340			5,518			10,609			10,265
Restructuring charge		—			—			747			—
Total costs and operating expenses		48,434			49,732			94,919			98,205
Loss from operations		(7,413	)		(7,682	)		(15,131	)		(11,322	)
Other income (expense):
Interest income		116			258			248			798
Interest expense		(72	)		(1	)		(148	)		(2	)
Foreign currency exchange gain (loss) and other		415			(66	)		431			677
Other income, net		459			191			531			1,473
Loss before income tax benefit (expense)		(6,954	)		(7,491	)		(14,600	)		(9,849	)
Income tax benefit (expense)		175			(204	)		219			136
Net loss	$	(6,779	)	$	(7,695	)	$	(14,381	)	$	(9,713	)
Basic and diluted net loss per share	$	(0.12	)	$	(0.13	)	$	(0.25	)	$	(0.17	)
Shares used in computing basic and diluted net loss per share		58,053			57,054			57,943			56,603

(1) See Note 11, “Restatement of Condensed Consolidated Financial Statements” in Notes to Condensed Consolidated Financial Statements.

The accompanying notes are an integral part of these Consolidated Financial Statements.

4

CEPHEID

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

(in thousands)

(unaudited)

	Six Months Ended June 30,
	2009			2008
				As Restated (1)
Cash flows from operating activities:
Net loss	$	(14,381	)	$	(9,713	)
Adjustments to reconcile net loss to net cash provided by operating activities:
Depreciation and amortization		4,110			3,727
Amortization of intangible assets		3,406			2,647
Amortization of prepaid compensation expense		126			126
Stock-based compensation related to employees and consulting services rendered		7,675			6,968
Unrealized gain on auction rate securities		(6,928	)		—
Unrealized loss on put option		6,519			—
Deferred rent		(1	)		376
Changes in operating assets and liabilities:
Accounts receivable		(1,876	)		2,690
Inventory		(1,925	)		(4,419	)
Prepaid expenses and other current assets		2,018			(1,239	)
Other non-current assets		426			(161	)
Accounts payable and other current liabilities		2,282			5,120
Accrued compensation		267			(210	)
Deferred revenue		6			(1,348	)
Net cash provided by operating activities		1,724			4,564
Cash flows from investing activities:
Capital expenditures		(2,823	)		(8,712	)
Payments for technology licenses		(1,500	)		—
Cost of acquisitions, net		(148	)		—
Proceeds from maturities of marketable securities and short-term investments		25			2,550
Proceeds from the sale of fixed assets		15			125
Transfer to unrestricted cash		1,500			517
Net cash used in investing activities		(2,931	)		(5,520	)
Cash flows from financing activities:
Net proceeds from the issuance of common shares and exercise of stock options		2,383			9,333
Principal payment of bank borrowing		(40	)		—
Principal payment of note payable		—			(4	)
Net cash provided by financing activities		2,343			9,329
Effect of exchange rate change on cash		112			17
Net increase in cash and cash equivalents		1,248			8,390
Cash and cash equivalents at beginning of period		23,478			16,476
Cash and cash equivalents at end of period	$	24,726		$	24,866

(1) See Note 11, “Restatement of Condensed Consolidated Financial Statements” in Notes to Condensed Consolidated Financial Statements.

The accompanying notes are an integral part of these Consolidated Financial Statements.

5

CEPHEID

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

1. Organization and Summary of Significant Accounting Policies

Organization and Business

Cepheid (the “Company” or “we”) was incorporated in the State of California on March 4, 1996. The Company is a broad-based molecular diagnostics company that develops, manufactures, and markets fully-integrated systems for testing in the Clinical market, as well as for application in the Company’s legacy Industrial, Biothreat and Partner markets. The Company’s systems enable rapid, sophisticated molecular testing for organisms and genetic-based diseases by automating otherwise complex manual laboratory procedures.

The condensed consolidated balance sheet at June 30, 2009, the condensed consolidated statements of operations for the three and six months ended June 30, 2009 and 2008, and the condensed consolidated statements of cash flows for the six months ended June 30, 2009 and 2008 are unaudited. In the opinion of management, these condensed consolidated financial statements reflect all adjustments that we consider necessary for a fair presentation of our financial position at such dates and the operating results and cash flows for those periods. Such adjustments include normal recurring adjustments and the correction of an error related to patent license amortization, for which the cumulative adjustments to our second quarter of fiscal year 2009 opening condensed consolidated balance sheet and to the opening December 31, 2008 condensed consolidated balance sheet are $3.3 million and $3.1 million, respectively. Please refer to Note 11 for further discussion. The accompanying condensed consolidated financial statements have been prepared in conformity with accounting principles generally accepted in the United States. However, certain information or footnote disclosures normally included in financial statements prepared in accordance with generally accepted accounting principles have been condensed or omitted pursuant to the rules and regulations of the Securities and Exchange Commission (“SEC”). The results of operations for such periods are not necessarily indicative of the results expected for the remainder of 2009 or for any future period. The condensed consolidated balance sheet as of December 31, 2008 is derived from audited financial statements as of that date with the patent license amortization adjustment but does not include all of the information and footnotes required by accounting principles generally accepted in the United States for complete financial statements. These condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and related notes included in our Annual Report on Form 10-K for the fiscal year ended December 31, 2008 filed with the SEC. Certain amounts have been reclassified to conform to the current period presentation.

In May 2009, the Financial Accounting Standards Board (“FASB”) issued Statement of Financial Accounting Standards (“SFAS”) No. 165, “Subsequent Events” (“SFAS 165”), which established general accounting standards and disclosure for subsequent events. The Company adopted SFAS No. 165 during the second quarter of 2009. In accordance with SFAS No. 165, the Company has evaluated subsequent events through the date and time the financial statements were issued, August 4, 2009.

Principles of Consolidation

The condensed consolidated financial statements include the accounts of the Company and its wholly-owned subsidiaries after elimination of intercompany transactions and balances. All gains and losses realized from foreign currency transactions denominated in currencies other than the foreign subsidiary’s functional currency are included in foreign currency exchange gain and other. Adjustments resulting from translating the financial statements of foreign subsidiaries into United States (“U.S.”) dollars are reported as a separate component of accumulated other comprehensive income (loss) in shareholders’ equity. The assets and liabilities of the Company’s foreign subsidiaries are translated from their respective functional currencies into U.S. dollars at the rates in effect at the balance sheet date, and revenue and expense amounts are translated at weighted average rates during the period.

Use of Estimates

The preparation of consolidated financial statements in conformity with U.S. generally accepted accounting principles (“GAAP”) requires management to make estimates and assumptions that affect the amounts reported in the consolidated financial statements and accompanying notes. Actual results could differ from these estimates.

Fair Value of Financial Instruments

In September 2006, the FASB issued Statement of Financial Accounting Standards No. 157, “Fair Value Measurements” (“SFAS 157”), which establishes guidelines for measuring fair value and expands disclosures regarding fair value measurements.

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SFAS 157 does not require any new fair value measurements but rather eliminates inconsistencies in guidance found in various prior accounting pronouncements and is effective for fiscal years beginning after November 15, 2007. In February 2008, the FASB issued FASB Staff Position (“FSP”) No. 157-2, “Effective Date of FASB Statement No. 157”, which provides a one year deferral of the effective date of SFAS 157 for non-financial assets and non-financial liabilities, except those that are recognized or disclosed in the financial statements at fair value at least annually, until fiscal years beginning after November 15, 2008, and interim periods within those fiscal years. Therefore, we adopted the provisions of SFAS 157 with respect to our financial assets and liabilities effective for fiscal years beginning after November 15, 2007 and we adopted the provisions of SFAS 157 with respect to our non-financial assets and non-financial liabilities effective for fiscal years beginning after November 15, 2008. The adoption of SFAS 157 did not have a material impact on our consolidated financial position, results of operations, or cash flows. See Note 2 for information and related disclosures regarding our fair value measurements.

In February 2007, the FASB issued SFAS No. 159, “The Fair Value Option for Financial Assets and Financial Liabilities — Including an Amendment of FASB Statement No. 115” (“SFAS 159”). The fair value option established by SFAS 159 permits all entities to choose to measure eligible items at fair value at specified election dates. A business entity will report unrealized gains and losses on items for which the fair value option has been elected in earnings (or another performance indicator if the business entity does not report earnings) at each subsequent reporting date. The fair value option: (a) may be applied instrument by instrument, with a few exceptions, such as investments otherwise accounted for by the equity method; (b) is irrevocable (unless a new election date occurs); and (c) is applied only to entire instruments and not to portions of instruments. We adopted SFAS 159 effective November 10, 2008. See Note 2 for information regarding our fair value measurements on financial assets. The adoption of SFAS 159 did not have a material impact on our financial condition, results of operations or cash flows since we did not elect to apply the fair value option for any of its eligible financial instruments or other items on the November 10, 2008 effective date.

Cash, Cash Equivalents and Short-Term Investments

Cash and cash equivalents consist of cash on deposit with banks, money market instruments, commercial paper and debt securities with maturities from the date of purchase of 90 days or less. Interest income includes interest, dividends, amortization of purchase premiums and discounts and realized gains and losses on sales of securities.

The Company designates marketable securities and short-term investments as either trading or available-for-sale and records them at fair value. Realized and unrealized gains and losses on investments are determined on the specific identification method. If designated as a trading security, unrealized gains and losses are recorded to current period operating results. If designated as an available-for-sale security, unrealized holding gains or losses are reported as a component of accumulated other comprehensive income (loss). Marketable securities and short-term investments with maturities greater than 90 days and less than one year are classified as short-term; otherwise they are classified as long-term. When an investment is sold, we report the difference between the sales proceeds and its carrying value (determined based on specific identification) as a capital gain or loss. An impairment charge is recognized when the decline in the fair value of a security below the amortized cost basis is determined to be other-than-temporary. The Company considers various factors in determining whether to recognize an impairment charge, including the duration of time and the severity to which the fair value has been less than our amortized cost basis, any adverse changes in the investees’ financial condition and the Company’s intent and ability to hold the investment for a period of time sufficient to allow for any anticipated recovery in market value.

Auction Rate Securities

At June 30, 2009, our short-term investments consisted of a portfolio of auction rate securities with a cost basis of $25.0 million, which are classified as trading securities and recorded at fair value in accordance with SFAS No. 115, “Accounting for Certain Investments in Debt and Equity Securities”, FSP FAS 115-2 and FAS 124-2, “Recognition and Presentation of Other-Than-Temporary Impairment” (“FSP 115-2/124-2”). The historical cost basis of this portfolio has been reduced by cumulative net losses on these securities of $3.0 million, which is comprised of a $9.9 million loss in 2008, a $3.0 million gain in the first quarter of 2009 and a $3.9 million gain in the second quarter of 2009. We valued these securities using a discounted cash flow methodology with significant inputs that included credit quality of the issuer, the percentage and the types of guarantees, contractual maturity, the timing and probability of the auction succeeding or security being called and discount factors. Our auction rate securities have failed to settle at auction since March 2008. We continue to collect interest on the investments that failed to settle at auction at the maximum contractual rate. At June 30, 2009, all but three of our auction rate securities continue to carry at least an AAA rating by at least one of the major rating agencies. Our auction rate securities consist of investments that are backed by pools of student loans, which are principally guaranteed by the Federal Family Educational Loan Program (“FFELP”), or insured.

On November 10, 2008, we accepted a comprehensive settlement arrangement offered by UBS, the fund manager with which we hold our auction rate securities. Under the settlement, we will have the option (“the put option”) to sell the auction rate securities held in our accounts with UBS to UBS at par value during the period beginning June 30, 2010 and ending July 2, 2012

7

(“put option exercise period”). In accepting the settlement arrangement, we also granted UBS the right to sell our auction rate securities at par at any time up until the expiration date of the rights and released UBS from any claims related to marketing and selling the auction rate securities, other than claims for consequential damages. Since the settlement agreement is a legally enforceable firm commitment, the put option is recognized as a financial asset at fair value in our financial statements, and accounted for separately from the associated securities. The fair value of the put option is based on the difference in value between the par value and the fair value of the associated auction rate securities. We have elected to measure the put option at its fair value pursuant to SFAS 159, and subsequent changes in fair value will also be recognized in respective period financial results. Since we intend to exercise the put option during the put option exercise period, we do not have the intent to hold the associated auction rate securities until recovery or maturity. We have classified these securities as trading pursuant to SFAS No. 115, “Accounting for Certain Investments in Debt and Equity Securities” (SFAS 115), which requires changes in the fair value of these securities to be recorded in respective period financial results, which we believe will substantially offset changes in the fair value of the put option. In addition, the rights permitted us to establish a demand revolving credit line, payable on demand, in an amount up to 75% of fair value of the securities at a net no cost, meaning that the interest we pay on the credit line will not exceed the interest that we receive on the auction rate securities that we have pledged as security for the credit line. We borrowed $14.7 million on the line of credit on November 10, 2008. Additionally, under the terms of the settlement agreement, if UBS is able to sell our auction rate securities at par, proceeds would be utilized to first repay any outstanding balance under the demand revolving credit line. We are still able to sell the auction rate securities, but in such a circumstance, if we sold at less than par, we would not be entitled to recover the par value support from UBS.

In the second quarter of 2009, we recorded a gain of $3.9 million related to the increase in value of our auction rate securities investments classified as trading securities, offset by a loss of $3.4 million on the put option. In the first six months of 2009, we recorded a gain of $6.9 million related to the increase in value of our auction rate securities investments classified as trading securities, offset by a loss of $6.5 million on the put option.

Restricted Cash

The $1.5 million of restricted cash as of December 31, 2008 consisted of a certificate of deposit with a maturity of less than 90 days held by a bank as collateral for our hedging program. During the first quarter of 2009 the Company engaged a different financial institution which did not require collateral for its hedging program.

Inventory

Inventory is stated at the lower of standard cost (which approximates actual cost) or market, with cost determined on the first-in-first-out method. Accordingly, allocation of fixed production overheads to conversion costs is based on normal capacity of the production. Abnormal amounts of idle facility expense, freight, handling costs and spoilage are expensed as incurred and not included in overhead. In addition, stock-based compensation cost of approximately $1.4 million and $1.6 million was included in inventory as of June 30, 2009 and December 31, 2008, respectively.

The components of inventory were as follows (in thousands):

	June 30, 2009		December 31, 2008
Raw Materials	$	14,140	$	12,328
Work in Process		10,663		8,629
Finished Goods		10,448		12,541
	$	35,251	$	33,498

Warranty Reserve

The Company warrants its systems to be free from defects for a period of 12 to 15 months from the date of sale and its disposable products to be free from defects, when handled according to product specifications, for the stated life of such products. Accordingly, a provision for the estimated cost of warranty repair or replacement is recorded at the time revenue is recognized. The Company’s warranty provision is established using management’s estimate of future failure rates and of the future costs of repairing any system failures during the warranty period or replacing any disposable products with defects. The activities in the warranty provision consisted of the following (in thousands):

	Three Months Ended June 30,						Six Months Ended June 30,
	2009			2008			2009			2008
Balance at beginning of period	$	665		$	704		$	655		$	549
Costs incurred and charged against reserve		96			(342	)		(328	)		(519	)
Accrual related to current period product sales		31			428			556			715
Adjustment to pre-existing warranties		(142	)		(40	)		(233	)		5
Balance at end of period	$	650		$	750		$	650		$	750

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Revenue Recognition

In accordance with Staff Accounting Bulletin (“SAB”) No. 104, “Revenue Recognition”, the Company recognizes revenue from product sales when there is persuasive evidence that an arrangement exists, delivery has occurred, the price is fixed or determinable and collectibility is reasonably assured. No right of return exists for the Company’s products except in the case of damaged goods. The Company has not experienced any significant returns of its products. Contract revenues include fees for technology licenses and research and development services, royalties under license and collaboration agreements. Contract revenue related to technology licenses is generally fully recognized only after the license period has commenced, the technology has been delivered and no further involvement of the Company is required. When the Company has continuing involvement related to a technology license, revenue is recognized over the license term. Royalties are typically based on licensees’ net sales of products that utilize the Company’s technology, and royalty revenues are recognized as earned in accordance with the contract terms when the royalties can be reliably measured and their collectibility is reasonably assured, such as upon the receipt of a royalty statement from the customer. Service revenue is recognized when the services have been provided. Shipping and handling costs are expensed as incurred and included in cost of product sales. In those cases where the Company bills shipping and handling costs to customers, the amounts billed are classified as revenue.

The Company recognizes revenue from both one-time product sales and longer-term contract arrangements. From time to time, the Company enters into revenue arrangements with multiple deliverables. Multiple element revenue agreements are evaluated under Emerging Issues Task Force (“EITF”) Issue No. 00-21, “Revenue Arrangements with Multiple Deliverables” (“EITF 00-21”), to determine whether the delivered item has value to the customer on a stand-alone basis and whether objective and reliable evidence of the fair value of the undelivered item exists. Deliverables in an arrangement that do not meet the separation criteria in EITF 00-21 must be treated as one unit of accounting for purposes of revenue recognition. Advance payments received in excess of amounts earned, such as funds received in advance of products to be delivered or services to be performed, are classified as deferred revenue until earned.

Grants and government sponsored research revenue and contract revenue related to research and development services are recognized as the related services are performed based on the performance requirements of the relevant contract. Under such agreements, the Company is required to perform specific research and development activities and is compensated either based on the costs or costs plus a mark-up associated with each specific contract over the term of the agreement or when certain milestones are achieved and recoverability is reasonably assured.

Foreign Currency Hedging

The Company accounts for derivative instruments in accordance with Statement of Financial Accounting Standards (“SFAS”) No. 133, “Accounting for Derivative Instruments and Hedging Activities”, SFAS No. 138, “Accounting for Certain Derivative Instruments and Certain Hedging Activities—an amendment of SFAS No. 133” and SFAS No. 149, “Amendment of Statement 133 on Derivative Instruments and Hedging Activities”. SFAS No. 133, 138, and 149 require that all derivatives, including foreign exchange contracts, be recognized in the balance sheet in other assets or liabilities at their fair value. The Company utilizes forward foreign exchange contracts in order to reduce the impact of fluctuations in the value of non-functional currency monetary assets and liabilities upon its financial statements and cash flows. These instruments are used to hedge foreign currency exposures of underlying non-functional currency monetary assets and liabilities primarily arising from intercompany transactions such as intercompany inventory purchases between Cepheid, Inc. and its foreign subsidiaries. These foreign exchange contracts, carried at fair value, have a maturity of 6 months or less. The Company’s accounting policies for these instruments are based on whether they meet the criteria for designation as hedging transactions. These foreign exchange contracts did not meet the criteria for hedging transactions, therefore, the Company has not elected special hedge accounting treatment under SFAS 133 and changes in fair value of the derivatives that are not designated as hedging instruments are recorded in earnings. The Company enters into approximately two derivatives per quarter ranging from $0.4 million to $10.0 million in notional value each with a total notional value of approximately $9.4 million in second quarter of 2009 and $11 million in first quarter of 2009. As of June 30, 2009, we had two outstanding foreign exchange forward contracts that were not designated as hedging instruments. These foreign exchange forward contracts were recorded as a derivative asset within Prepaid expenses and other current assets with a fair value of

9

approximately $40,000, representing the estimated gain on those outstanding foreign currency exchange forward contracts as of June 30, 2009, and a derivative liability within Accrued and other liabilities with a fair value of approximately $10,000, representing the estimated loss on those outstanding foreign currency exchange forward contracts as of June 30, 2009. During the three and six months ended June 30, 2009, the effect of our hedging transactions, consisting entirely of foreign currency forward contracts, on our condensed consolidated statement of operations was a pre-tax loss of approximately $0.4 million and $0.3 million, respectively.

Net Loss per Share

Basic net loss per share has been calculated based on the weighted-average number of common shares outstanding during the period. Shares used in diluted net loss per share calculations exclude anti-dilutive common stock equivalent shares, consisting of stock options. These anti-dilutive common stock equivalent shares totaled 8,070,000 and 5,705,000 for the three months ended June 30, 2009 and 2008, respectively, and 8,028,000 and 5,584,000 for the six months ended June 30, 2009 and 2008, respectively.

Comprehensive Loss

Comprehensive loss includes net loss as well as other comprehensive income (loss). The Company’s other comprehensive income (loss) consists of foreign currency translation adjustments and unrealized gains (losses) on available-for-sale securities. The following table presents the calculation of comprehensive loss, including components of other comprehensive loss (in thousands):

	Three Months Ended June 30,						Six Months Ended June 30,					��
	2009			2008			2009			2008
Net loss	$	(6,779	)	$	(7,695	)	$	(14,381	)	$	(9,713	)
Other comprehensive income (loss):
Foreign currency translation adjustments		16			(46	)		58			288
Unrealized loss on available for sale investments		—			(873	)		—			(3,017	)
Comprehensive loss	$	(6,763	)	$	(8,614	)	$	(14,323	)	$	(12,442	)

Recent Accounting Pronouncements

In September 2006, the FASB issued SFAS No. 157, “Fair Value Measurements” (“SFAS 157”), which defines fair value, establishes guidelines for measuring fair value and expands disclosures regarding fair value measurements. SFAS 157 does not require any new fair value measurements but rather eliminates inconsistencies in guidance found in various prior accounting pronouncements and is effective for fiscal years beginning after November 15, 2007. In February 2008, the FASB issued FSP No. 157-2, “Effective Date of FASB Statement No. 157” (“FSP No. 157-2”). FSP No. 157-2 provides a one year deferral of the effective date of SFAS No. 157 for nonfinancial assets and nonfinancial liabilities, except those that are recognized or disclosed at fair value in the financial statements on a recurring basis (at least annually) until fiscal years beginning after November 15, 2008, and interim periods within those fiscal years. We adopted SFAS 157 for all nonfinancial assets and nonfinancial liabilities measured at fair value on a non-recurring basis for fiscal years beginning after November 15, 2008. The adoption of SFAS 157 did not have a significant impact on the Company’s consolidated financial position, results of operations or cash flows. We will adopt SFAS 157 for all non-financial assets and nonfinancial liabilities in the first quarter of fiscal 2010. Although the Company will continue to evaluate the application of SFAS 157 to nonfinancial assets and nonfinancial liabilities, we do not expect the adoption of SFAS 157 with respect to nonfinancial assets and nonfinancial liabilities will have a material impact on Company’s consolidated financial position, results of operations or cash flows.

In December 2007, the FASB issued SFAS No. 141(R), “Business Combinations” (“SFAS 141(R)”), and SFAS No. 160, “Non-Controlling Interests in Consolidated Financial Statements—an Amendment of ARB No. 51” (“SFAS 160”). SFAS 141(R) changes how business acquisitions are accounted for and impacts financial statements both on the acquisition date and in subsequent periods. SFAS 160 changes the accounting and reporting for minority interests, which are recharacterized as noncontrolling interests and classified as a component of equity. We adopted SFAS No. 141(R) and SFAS No. 160 on January 1, 2009. The Company does not currently have any non-controlling interests in its subsidiaries, and accordingly the adoption of SFAS No. 160 did not have a material impact on the Company’s financial statements. The Company adopted SFAS 141(R) on January 1, 2009 and the adoption did not have a significant impact on the Company’s consolidated financial position, results of operations or cash flows. However, if the Company enters into material business combinations in the future, a transaction may significantly impact the Company’s consolidated financial position and results of operations as compared to the Company’s recent acquisitions, accounted for under prior GAAP requirements, due to the changes described above.

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In March 2008, the FASB issued SFAS No. 161 “Disclosures about Derivative Instruments and Hedging Activities—an amendment of FASB Statement No. 133” (“SFAS 161”), which requires companies with derivative instruments to disclose information that should enable financial statement users to understand how and why a company uses derivative instruments, how derivative instruments and related hedged items are accounted for under SFAS 133 and how derivative instruments and related hedged items affect a company’s financial position, financial performance and cash flows. We adopted SFAS 161 in the first quarter of fiscal 2009. Since SFAS 161 only required additional disclosure, the adoption did not impact the Company’s consolidated financial position, results of operations or cash flows.

In April 2008, the FASB issued FSP No. 142-3, “Determination of the Useful Life of Intangible Assets” (“FSP 142-3”). FSP 142-3 amends the factors an entity should consider in developing renewal or extension assumptions used in determining the useful life of recognized intangible assets under SFAS No. 142, “Goodwill and Other Intangible Assets.” This new guidance applies prospectively to intangible assets that are acquired individually or with a group of other assets in business combinations and asset acquisitions. FSP 142-3 is effective for financial statements issued for fiscal years and interim periods beginning after December 15, 2008. The Company adopted FSP 142-3 on January 1, 2009 and the adoption did not have a significant impact on the Company’s consolidated financial position, results of operations or cash flows. However, if the Company enters into material business combinations after the adoption of SFAS No. 142-3, a transaction may significantly impact the Company’s consolidated financial position and results of operations as compared to the Company’s recent acquisitions, accounted for under prior GAAP requirements, due to the changes described above.

In April 2009, the FASB issued FSP FAS 157-4, “Determining Fair Value When Volume and Level of Activity for the Asset or Liability Have Significantly Decreased and Identifying Transactions That Are Not Orderly” (“FSP 157-4”). FSP 157-4 provides guidance on how to determine the fair value of assets and liabilities when the volume and level of activity for the asset/liability has significantly decreased. FSP 157-4 also provides guidance on identifying circumstances that indicate a transaction is not orderly. In addition, FSP 157-4 requires disclosure in interim and annual periods of the inputs and valuation techniques used to measure fair value and a discussion of changes in valuation techniques. We adopted FSP 157-4 in the second quarter of fiscal year 2009. The adoption of FSP 157-4 did not have a significant impact on our consolidated financial statements.

In April 2009, the FASB issued FSP FAS 115-2 and FAS 124-2, “Recognition and Presentation of Other-Than-Temporary Impairment” (“FSP 115-2/124-2”). FSP 115-2/124-2 amends the requirements for the recognition and measurement of other-than-temporary impairments for debt securities by modifying the pre-existing “intent and ability” indicator. Under FSP 115-2/124-2, an other-than-temporary impairment is triggered when there is an intent to sell the security, it is more likely than not that the security will be required to be sold before recovery, or the security is not expected to recover the entire amortized cost basis of the security. Additionally, FSP 115-2/124-2 changes the presentation of an other-than-temporary impairment in the statement of operations for those impairments involving credit losses. The credit loss component will be recognized in earnings and the remainder of the impairment will be recorded in other comprehensive income. We adopted FSP 115-2/124-2 in the second quarter of fiscal year 2009 and the adoption did not have a significant impact on our consolidated financial statements.

In April 2009, the FASB issued FSP FAS 107-1 and APB 28-1, “Interim Disclosure about Fair Value of Financial Instruments” (“FSP 107-1/APB 28-1”). FSP 107-1/APB 28-1 requires interim disclosures regarding the fair values of financial instruments that are within the scope of FAS 107, “Disclosures about the Fair Value of Financial Instruments.” Additionally, FSP 107-1/APB 28-1 requires disclosure of the methods and significant assumptions used to estimate the fair value of financial instruments on an interim basis as well as changes in the methods and significant assumptions from prior periods. FSP 107-1/APB 28-1 does not change the accounting treatment for these financial instruments. We adopted FSP 107-1/APB 28-1 in the second quarter of fiscal year 2009.

In April 2009, the FASB issued FSP SFAS 141(R)-1, “Accounting for Assets Acquired and Liabilities Assumed in a Business Combination That Arise from Contingencies” (“FSP SFAS 141(R)-1”). FSP SFAS 141(R)-1 addresses application issues on initial recognition and measurement, subsequent measurement and accounting, and disclosure of assets and liabilities arising from contingencies in a business combination. FSP SFAS 141(R)-1 is effective for assets or liabilities arising from contingencies in business combinations for which the acquisition date is on or after the beginning of the first annual reporting period beginning on or after December 15, 2008. We adopted FSP SFAS 141(R)-1 in the second quarter of fiscal 2009. The adoption did not have a significant impact on the Company’s consolidated financial position, results of operations or cash flows. If the Company enters into material business combinations after the adoption of SFAS No. 141(R), a transaction may significantly impact the Company’s consolidated financial position and results of operations as compared to the Company’s recent acquisitions, accounted for under prior GAAP requirements, due to the changes described above.

In May 2009, the FASB issued SFAS No. 165, “Subsequent Events” (“SFAS 165”). SFAS 165 is intended to establish general standards of accounting for and disclosure of events that occur after the balance sheet date but before financial statements are issued or

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are available to be issued. It requires the disclosure of the date through which an entity has evaluated subsequent events and the basis for selecting that date, that is, whether that date represents the date the financial statements were issued or were available to be issued. SFAS 165 is effective for interim or annual financial periods ending after June 15, 2009. We adopted SFAS No. 165 in the second quarter of fiscal 2009. The adoption of SFAS 165 did not have a material impact on Company’s consolidated financial position, results of operations or cash flows.

The FASB has formally approved the FASB Accounting Standards Codification (“Codification”) as the single source of authoritative U.S. accounting and reporting standards, other than guidance issued by the SEC. The codification will be effective for interim and annual periods ending on or after September 15, 2009. At that time, the Codification will supersede all then-existing non-SEC accounting and reporting standards. All other non-grandfathered, non-SEC accounting literature not included in the Codification will become nonauthoritative. The FASB’s primary goal in developing the Codification is to simplify user access to all authoritative U.S. GAAP by providing all the authoritative literature related to a particular accounting topic in one place. Following the FASB Board’s approval of the Codification as the single source of non-SEC authoritative accounting and reporting standards, the FASB will no longer consider new standards as authoritative in their own right. Instead, the new standards will serve only to provide background information about the issue, update the Codification, and provide the basis for conclusions regarding the change in the Codification. Therefore, beginning with its third quarterly filing of 2009, all Company references made to U.S. GAAP will use the new Codification numbering system prescribed by the FASB. As the Codification is not intended to change or alter existing U.S. GAAP, it is not expected to have any impact on the Company’s consolidated financial statements.

2. Fair Value

SFAS 157 defines fair value, establishes a framework for measuring fair value under GAAP and requires enhanced disclosures about fair value measurements. Fair value is defined under SFAS 157 as the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date. Valuation techniques used to measure fair value under SFAS 157 must maximize the use of observable inputs and minimize the use of unobservable inputs. The standard describes a fair value hierarchy based on three levels of inputs, of which the first two are considered observable and the third unobservable. The three levels of inputs are the following:

• Level 1 - Quoted prices in active markets for identical assets or liabilities.

• Level 2 - Inputs other than Level 1 that are observable, either directly or indirectly, such as quoted prices for similar assets or liabilities; quoted prices in markets that are not active; or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities.

• Level 3 - Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities.

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In accordance with SFAS 157, the following table represents the fair value hierarchy for our financial assets (cash equivalents and short-term investments) and financial liabilities (foreign currency derivatives) measured at fair value on a recurring basis as of June 30, 2009 and December 31, 2008 (in thousands):

Balance as of June 30, 2009:

	Level 1		Level 2		Level 3		Total
Assets:
Cash	$	19,383	$	—	$	—	$	19,383
Cash equivalent - money market funds		5,343		—		—		5,343
Foreign currency derivatives		—		41		—		41
Short-term investments - taxable auction rate securities		—		—		22,004		22,004
Put option		—		—		2,920		2,920
Total	$	24,726	$	41	$	24,924	$	49,691
Liabilities:
Foreign currency derivatives		—	$	10		—	$	10
Total	$	—	$	10	$	—	$	10
Balance as of December 31, 2008:
	Level 1		Level 2		Level 3		Total
Assets:
Cash	$	18,252	$	—	$	—	$	18,252
Cash equivalent - money market funds		5,226		—		—		5,226
Investments - taxable auction rate securities		—		—		15,101		15,101
Put option		—		—		9,438		9,438
Total	$	23,478	$	—	$	24,539	$	48,017

Derivative assets and liabilities within the scope of SFAS No. 133, “Accounting for Derivative Instruments and Hedging Activities”, are required to be recorded at fair value. The Company’s derivatives that are impacted by SFAS No. 157 include foreign exchange forward contracts. The Company has elected to use the income approach to value the derivatives, using observable Level 2 market expectations at measurement date and standard valuation techniques to convert future amounts to a single present amount assuming that participants are motivated, but not compelled to transact.

Level 2 inputs for the valuations are limited to quoted prices for similar assets or liabilities in active markets (specifically foreign currency spot rate and forward points) and inputs other than quoted prices that are observable for the asset or liability (specifically LIBOR rates, credit default spot rates, and company specific LIBOR spread). Mid-market pricing is used as a practical expedient for fair value measurements. SFAS No. 157 states that the fair value measurement of an asset or liability must reflect the nonperformance risk of the entity and the counterparty. Therefore, the impact of the counterparty’s creditworthiness when in an asset position and the Company’s creditworthiness when in a liability position has also been factored into the fair value measurement of the derivative instruments and did not have a material impact on the fair value of these derivative instruments. Both the counterparty and the Company are expected to continue to perform under the contractual terms of the instruments.

Level 3 assets consist of auction rate securities whose underlying assets are student loans, most of which are guaranteed by the federal government. In February 2008, auctions began to fail for these securities, and each auction since then has failed. Based on the overall failure rate of these auctions, the frequency of the failures, and the underlying maturities of the securities, a portion of which are greater than 30 years, we had classified the auction rate securities as long-term assets on our consolidated balance sheet as of December 31, 2008. Our put option allows us to sell the auction rate securities held in our accounts with UBS to UBS at par value beginning on June 30, 2010. Therefore, as of June 30, 2009, we have reclassified the auction rate securities to current assets on our condensed consolidated balance sheet. These investments were valued at fair value as of June 30, 2009. The following table provides a summary of changes in fair value of our auction rate securities and put option for the six-month periods ended June 30, 2009 and, 2008 (in thousands):

				Level 3
Balance at January 1, 2009				$	24,539
Sale					(25	)
Unrealized gain of auction rate securities included in current period earnings					6,928
Unrealized loss of put option included in current period earnings					(6,518	)
Balance at June 30, 2009				$	24,924
	Level 1			Level 3
Balance at January 1, 2008	$	27,550		$	—
Net settlements		(2,550	)		—
Transfer		(25,000	)		25,000
Unrealized loss included in accumulated other comprehensive loss		—			(3,017	)
Balance at June 30, 2008	$	—		$	21,983

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Our investment portfolio of auction rate securities is structured with short-term interest rate reset dates of generally less than 30 days, but with contractual maturities that are well in excess of ten years. Our auction rate securities consist of investments that are backed by pools of student loans, which are principally guaranteed by the Federal Family Educational Loan Program (“FFELP”), or insured. We believe that the credit quality of these securities is high based on these guarantees. We determined the fair market values of our financial instruments based on the fair value hierarchy established in SFAS 157, which requires an entity to maximize the use of observable inputs (Level 1 and Level 2 inputs) and minimize the use of unobservable inputs (Level 3 inputs) when measuring fair value. Until the first quarter of 2008, the fair values of our auction rate securities were determinable by reference to frequent successful Dutch auctions of such securities, which settled at par. Therefore, at the adoption date, we had categorized our investments in auction rate securities as Level 1. Given the current failures in the auction markets to provide quoted market prices of the securities, as well as the lack of any correlation of these instruments to other observable market data, we valued these securities using a discounted cash flow methodology with the most significant input categorized as Level 3. Significant inputs that went into the model were the credit quality of the issuer, the percentage and the types of guarantees, contractual maturity, the timing and probability of the auction succeeding or the security being called and discount factors.

On November 10, 2008, we accepted a comprehensive settlement arrangement offered by UBS, the fund manager with which we hold our auction rate securities. Under the settlement, we will have the option (“the put option”) to sell the auction rate securities held in our accounts with UBS to UBS at par value during the period beginning June 30, 2010 and ending July 2, 2012. In accepting the settlement arrangement, we also granted UBS the right to sell our auction rate securities at par at any time up until the expiration date of the rights and released UBS from any claims related to the marketing and sale of auction rate securities, other than claims for consequential damages. Since the settlement agreement is a legally enforceable firm commitment, the put option is recognized as a financial asset at fair value in our financial statements, and accounted for separately from the associated securities. The fair value of the put option is based on the difference in value between the par value and the fair value of the associated auction rate securities. We have elected to measure the put option at its fair value pursuant to SFAS 159 and subsequent changes in fair value will also be recognized in current period earnings. Since we intend to exercise the put option during the period beginning June 30, 2010 and ending July 2, 2012, we do not have the intent to hold the associated auction rate securities until recovery or maturity. We have classified these securities as trading pursuant to SFAS 115, which requires changes in the fair value of these securities to be recorded in current period earnings, which we believe will substantially offset changes in the fair value of the put option. In addition, the rights permitted us to establish a demand revolving credit line in an amount equal to the par value of the securities at a net no cost. We are still able to sell the auction rate securities on our own, but in such a circumstance, we would lose the par value support from UBS.

In the second quarter of 2009, we recorded a gain to other income, net of $3.9 million to increase the value of our auction rate securities investments classified as trading securities, offset by a loss of $3.4 million of the estimated fair value of the put option. In the first six months of 2009, we recorded a gain to other income, net of $6.9 million to increase the value of our auction rate securities investments classified as trading securities, offset by a loss of $6.5 million of the estimated fair value of the put option.

In accordance with the provisions of SFAS 107, “Disclosure about Fair Value of Financial Instruments” (“SFAS 107”), at both June 30, 2009 and December 31, 2008, the fair value of the Company’s “no net cost” payable on demand loan was estimated at approximately $14.6 million, which approximates its carrying value.

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3. Intangible Assets

Intangible assets related to licenses are recorded at cost, less accumulated amortization. Intangible assets related to technology and other intangible assets acquired in acquisitions are recorded at fair value at the date of acquisition, less accumulated amortization. Intangible assets are amortized over their estimated useful lives, ranging from 3 to 20 years, on a straight-line basis, except for intangible assets acquired in the acquisitions of Actigenics, Sangtec, Stretton and Alpha-Omega, which are amortized on the basis of economic useful life. Amortization of intangible assets is primarily included in cost of product sales in the accompanying condensed consolidated statements of operations.

See Note 11 for information and related disclosures regarding our prior period adjustment in the current quarter financial statements related to patent license amortization which decreased the opening balance of intangible assets, net and increased the accumulated deficit by $3.3 million for the second quarter of fiscal year 2009.

The recorded value and accumulated amortization of major classes of intangible assets at June 30, 2009 were as follows (in thousands):

	Recorded Value		Accumulated Amortization			Net Book Value
Licenses	$	44,507	$	(19,194	)	$	25,313
Technology acquired in acquisitions		8,613		(1,466	)		7,147
Other		3,183		(1,408	)		1,775
	$	56,303	$	(22,068	)	$	34,235

Included in licenses was $19.9 million in connection with a patent license agreement with F. Hoffman-La Roche Ltd., effective July 1, 2004. The net book value of this license was $10.0 million and $11.0 million at June 30, 2009 and December 31, 2008, respectively, including the patent license amortization adjustment.

Amortization expense of intangible assets was $1.7 million and $1.3 million for the three months ended June 30, 2009 and 2008, respectively, and $3.4 million and $2.6 million for the six months ended June 30, 2009 and 2008, including the patent license amortization adjustment. The expected future annual amortization expense of intangible assets recorded on our condensed consolidated balance sheet as of June 30, 2009 is as follows, assuming no impairment charges (in thousands):

For the Years Ending December 31,	Amortization Expense
2009 (remaining six months)	$	3,418
2010		6,774
2011		6,667
2012		5,298
2013		4,589
Thereafter		7,489
Total expected future annual amortization	$	34,235

4. Segment and Significant Concentrations

We and our wholly owned subsidiaries operate in one business segment.

We currently sell our products through our direct sales force and through third-party distributors. There was one direct customer that accounted for 19% and 25% of total product sales for the three months ended June 30, 2009 and 2008, respectively, and 20% and 28% of total product sales for the six months ended June 30, 2009 and 2008, respectively, and one other direct customer accounted for 1% and 9% of total product sales for the three months ended June 30, 2009 and 2008, respectively, and less than 1% and 11% of total product sales for the six months ended June 30, 2009 and 2008, respectively. We have distribution agreements with several companies to distribute products in the U.S. and have several regional distribution arrangements throughout Europe, Japan, South Korea, China, Mexico and other parts of the world. There was one customer whose accounts receivable balance represented 12% and 14% of total receivables as of June 30, 2009 and December 31, 2008, respectively. The following table provides a breakdown of product sales by geographic region (in thousands):

	Three Months Ended June 30,						Six Months Ended June 30,
	2009		2008		% Change		2009		2008		% Change
Product Sales Geographic information:
North America
Clinical	$	20,145	$	15,498	30	%	$	38,513	$	28,310	36	%
Other		11,196		14,211	-21	%		22,025		32,823	-33	%
Total North America		31,341		29,709	5	%		60,538		61,133	-1	%
International
Clinical	$	6,517	$	4,770	37	%	$	11,933	$	9,606	24	%
Other		1,702		4,474	-62	%		3,677		10,134	-64	%
Total International		8,219		9,244	-11	%		15,610		19,740	-21	%
Total product sales	$	39,560	$	38,953	2	%	$	76,148	$	80,873	-6	%

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No single country outside of the United States represented more than 10% of our total revenues or total assets in any period presented.

5. Collaboration Profit Sharing

Collaboration profit sharing represents the amount that the Company pays to Applied Biosystems Group (“ABI”) (now Life Technologies Corporation) under our collaboration agreement to develop reagents for use in the Biohazard Detection System (“BDS”) developed for the United States Postal Service (“USPS”). Under the agreement, computed gross margin on anthrax cartridge sales are shared equally between the two parties. Collaboration profit sharing expense was $2.6 million and $2.8 million for the three months ended June 30, 2009 and 2008, respectively, and $5.2 million and $6.5 million for the six months ended June 30, 2009 and 2008, respectively. The total revenues and cost of sales related to these cartridge sales are included in the respective balances in the consolidated statement of operations.

6. Employee Equity Incentive Plans and Stock-Based Compensation Expense

On April 29, 2009, we held our 2009 Annual Meeting of Shareholders and the shareholders approved an amendment to our 2000 Employee Stock Purchase Plan to increase the number of shares issuable thereunder by 1,500,000 shares.

The stock-based compensation expense in the condensed consolidated statement of operations was as follows (in thousands):

	Three Months Ended June 30,				Six Months Ended June 30,
	2009		2008		2009		2008
Cost of product sales	$	728	$	246	$	1,082	$	596
Research and development		1,416		1,414		2,847		2,677
Sales and marketing		668		909		1,378		1,755
General and administrative		1,316		1,138		2,369		1,941
Total stock-based compensation expense	$	4,128	$	3,707	$	7,676	$	6,969

Stock-based compensation cost of approximately $1.4 million and $1.6 million was included in inventory as of June 30, 2009 and December 31, 2008, respectively.

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A summary of option activity under all plans is as follows:

	Shares		Weighted Average Exercise Price		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
Outstanding, December 31, 2008	9,006,286		$	11.72
Granted	1,452,370		$	8.59
Exercised	(223,204	)	$	4.32
Forfeited	(327,215	)	$	12.86
Outstanding, June 30, 2009	9,908,237		$	11.39	5.09	$	9,965,514
Exercisable, June 30, 2009	5,780,474		$	9.85	4.58	$	8,230,070
Vested and expected to vest, June 30, 2009	9,091,558		$	11.19	5.04	$	9,640,559

A summary of all award activity, which consists of RSAs, is as follows:

	Shares		Weighted Average Grant Date Fair Value
Outstanding, December 31, 2008	65,917		$	16.07
Granted	10,000			8.43
Vested	(13,750	)		15.19
Cancelled	—			—
Outstanding, June 30, 2009	62,167		$	15.04

The fair value of our stock options granted to employees and shares purchased by employees under the ESPP was estimated using the following assumptions:

	Three Months Ended June 30,				Six Months Ended June 30,
	2009		2008		2009		2008
OPTION SHARES:
Expected Term (in years)	4.52		4.46		4.52		4.52
Volatility	0.75		0.60		0.73		0.60
Expected Dividends	0.00	%	0.00	%	0.00	%	0.00	%
Risk Free Interest Rates	1.85	%	2.93	%	1.82	%	2.93	%
Estimated Forfeitures	8.14	%	7.74	%	7.94	%	7.27	%
ESPP SHARES:
Expected Term (in years)	1.25		1.25		1.25		1.25
Volatility	0.84		0.51		0.84		0.51
Expected Dividends	0.00	%	0.00	%	0.00	%	0.00	%
Risk Free Interest Rates	0.62	%	2.12	%	0.62	%	2.12	%

The weighted average fair value of our stock options granted to employees was $5.08 and $10.49 for the three months ended June 30, 2009 and 2008, respectively, and $5.01 and $10.98 for the six months ended June 30, 2009 and 2008. Also, the weighted average fair value for our shares purchased by employees under the ESPP was $3.60 and $11.55 for both the three and six months ended June 30, 2009 and 2008, respectively.

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7. Income Taxes

We have had no U.S. federal or state income tax provision for any period as we have incurred operating losses in all periods. The net income tax benefit of $0.2 million for the three and six months ended June 30, 2009 relates primarily to our United States estimated refundable research and development tax credits extended by the American Recovery Act of 2009 and signed into law in February 2009. The income tax expense for the three months ended June 30, 2008 of $0.2 million relates to foreign withholding tax. The net income tax benefit for the six months ended June 30, 2008 of $0.1 million relates to research and development tax credits associated with our French subsidiary, less the foreign withholding tax expense.

We utilize the liability method of accounting for income taxes as set forth in SFAS No. 109 (“SFAS 109”), “Accounting for Income Taxes”. Under the liability method, deferred taxes are determined based on the temporary differences between the financial statement and tax bases of assets and liabilities using enacted tax rates. Our position is to record a valuation allowance when it is more likely than not that some of the deferred tax assets will not be realized.

On February 20, 2009, California enacted tax legislation that may significantly impact the amount of future income or loss apportioned to the state for the Company. The changes are effective for years beginning on or after January 1, 2011. Under SFAS 109, the impact of a legislative tax change must be reflected in the quarter when it is enacted. Accordingly, the Company’s California deferred tax assets and liabilities, and expected future deferred California tax rate, should have been adjusted for the new California legislation in the current quarter. We are still evaluating the impact of the California-enacted tax legislation on our apportioned income to California and on the California deferred tax assets and liabilities. Due to the full valuation allowance, the change in California tax legislation will not have an impact on the provision and we do not currently believe this will impact the deferred tax assets net of valuation allowance.

For federal income tax purposes, the Company has open tax years from 1996 through 2008 due to net operating loss carryforwards relating to these years. Substantially all material state, local and foreign income tax matters have been concluded for years through December 31, 2001. For California state income tax purposes, the Company has open years from 2000 through 2008 due to either research credit carryovers or net operating loss carryforwards.

Effective January 1, 2007, we adopted the provisions of Financial Accounting Standards Interpretation No. 48 (“FIN 48”), “Accounting for Uncertainty in Income Taxes - An Interpretation of FASB Statement No. 109”. The Company’s policy is to recognize interest and penalties accrued on any unrecognized tax benefits as a component of income tax expense.

We recognize interest and penalties related to uncertain tax positions in income tax expense. For the periods presented, we did not recognize any interest or penalties related to uncertain tax positions in the condensed consolidated statements of operations, and at June 30, 2009 and June 30, 2008, we had no accrued interest or penalties.

Our total unrecognized tax benefit as of the January 1, 2007 adoption date and as of December 31, 2008 were $0.2 million and $4.3 million, respectively. Although unrecognized tax benefits for individual tax positions may have increased or decreased during the six months ended June 30, 2009, we do not currently believe that it is reasonably possible that there will be a significant increase or decrease in unrecognized tax benefits. Based on our analysis, no significant change to reserves has occurred in the six months ended June 30, 2009.

8. Commitments and Contingencies

In May 2009, we extended one of our long-term operating lease obligations for approximately 76,000 square feet of office and laboratory space in Sunnyvale, California from an expiration date of March 2012 to March 2015. Rent expense for all operating leases for both the three months ended June 30, 2009 and 2008 was $0.9 million, and $1.7 million and $1.6 million for the six months ended June 30, 2009 and 2008, respectively. Minimum annual rental commitments under facility operating leases as of June 30, 2009 are as follows (in thousands):

Years Ending December 31,
2009 (remaining six months)	$	1,843
2010		3,419
2111		2,718
2112		2,235
2113 and thereafter		4,196
Total minimum payments	$	14,411

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As of June 30, 2009, purchase commitments consisted of $5.8 million, $6.6 million, $2.5 million, $2.5 million and $2.5 million for the remainder of 2009, 2010, 2011, 2012 and 2013 respectively.

We have certain royalty commitments associated with the shipment and licensing of certain products. Royalty expense is generally based on a dollar amount per unit shipped or a percentage of the underlying revenue.

In the normal course of business, we provide indemnifications of varying scope to customers against claims of intellectual property infringement made by third parties arising from the use of our products. Historically, costs related to indemnification provisions have not been significant and we are unable to estimate the maximum potential impact of these indemnification provisions on our future results of operations.

To the extent permitted under California law, we have agreements whereby we indemnify our directors and officers for certain events or occurrences while the director or officer is, or was serving, at our request in such capacity. The indemnification period covers all pertinent events and occurrences during the director’s or officer’s service. The maximum potential amount of future payments we could be required to make under these indemnification agreements is not specified in the agreements; however, we have director and officer insurance coverage that reduces our exposure and enables us to recover a portion of any future amounts paid. We believe the estimated fair value of these indemnification agreements in excess of applicable insurance coverage is minimal.

We respond to claims arising in the ordinary course of business. In certain cases, management has accrued estimates of the amounts it expects to pay upon resolution of such matters, and such amounts are included in other accrued liabilities. Should we not be able to secure the terms it expects, these estimates may change and will be recognized in the period in which they are identified. Although the ultimate outcome of such claims is not presently determinable, management believes that the resolution of these matters will not have a material adverse effect on our financial position, results of operations and cash flows.

9. Derivative Instruments and Hedging Activities

The Company is exposed to global market risks, including the effect of changes in foreign currency exchange rates and uses derivatives to manage financial exposures that occur in the normal course of business. The Company does not hold or issue derivatives for trading or speculative purposes.

The Company enters into foreign exchange forward contracts to mitigate the change in fair value of our net recognized foreign currency assets and liabilities and to reduce the risk that our earnings and cash flows will be adversely affected by changes in exchange rates. These derivative instruments are not designated as hedging instruments under SFAS 133. Accordingly, changes in the fair value of these derivative instruments are recognized immediately in other (income) expense, net, on the statement of operations together with the transaction gain or loss from the hedged balance sheet position. These derivative instruments do not subject us to material balance sheet risk due to exchange rate movements because gains and losses on these derivatives are intended to offset gains and losses on the assets and liabilities being hedged.

The Company’s derivative financial instruments present certain market and counterparty risks; however, concentration of counterparty risk is mitigated as the Company deals with major banks with Standard & Poor’s and Moody’s long-term debt ratings of A or higher. In addition, only conventional derivative financial instruments are utilized. At this time, the Company does not require collateral or any other form of securitization to be furnished by the counterparties to its derivative financial instruments.

The fair value of derivative instruments in our consolidated balance sheet as of June 30, 2009 was as follows (in thousands):

	Fair Value of Derivative Instruments
	Asset Derivatives			Liability Derivatives
Category	Balance Sheet Location	Fair Value (assets)		Balance Sheet Location	Fair Value (liabilities)
Derivatives not designated as hedging instruments:
Forward exchange forward contracts	Prepaid expense and other current assets	$	41	Accrued and other liabilities	$	10

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The effect of derivative instruments on our consolidated statement of operations for three and six months ended June 30, 2009 was as follows (in thousands):

	Trade Type	Statement of Operations Location	Three Months Ended June 30, 2009			Six Months Ended June 30, 2009
Designation			Gain (Loss) Recognized			Gain (Loss) Recognized
Derivatives Not Designated as Hedging Instruments	Forward exchange forward contracts	Foreign currency exchange gain and other	$	(449	)	$	(291	)

For further information on the fair value of derivative instruments see Note 2: Fair Value.

10. Restructuring Charge

During the first quarter of 2009, we eliminated 47 positions that impacted employees, contractors and replacement positions, which resulted in $0.7 million of restructuring expense, mainly related to severance. As of June 30, 2009, we have no material outstanding restructuring expenses to be paid.

11. Restatement of Condensed Consolidated Financial Statements—Patent License Amortization

We capitalize patent licenses and amortize them over their estimated useful lives on a straight-line basis. Our internal periodic review of our patent license useful lives during the second quarter of 2009 identified that the useful lives of certain patents were miscalculated at the time those patents were acquired, thus those patent licenses were being amortized over incorrect useful lives. This error resulted in the understatement of amortization expense over several reporting periods, starting in 2004. In accordance with SAB No. 108, “Financial Statements – Considering the Effects of Prior Year Misstatements when Quantifying Misstatements in Current Year Financial Statements” (“SAB 108”), in assessing the identified error, we considered both the “rollover” approach, which quantifies misstatements originating in the current year statement of operations and the “iron curtain” approach, which quantifies misstatements based on the effects of correcting the misstatements existing in the balance sheet at the end of the reporting period. We believe the impact of the patent license amortization errors was not material to prior years’ statements of operations under the rollover approach. However, under the iron curtain method, the cumulative patent license amortization errors were material to our fiscal year 2009 condensed consolidated financial statements and we have therefore restated the condensed consolidated statement of operations for the three and six month periods ended June 30, 2008, the condensed consolidated statement of cash flows for the six months ended June 30, 2008, and the condensed consolidated balance sheet at December 31, 2008. The Company recognized the cumulative effect of the adjustments to assets as of the beginning of the second quarter of fiscal year 2009 and the offsetting adjustment to the opening balance of accumulated deficit for the second quarter of fiscal year 2009. We recognized the following cumulative adjustment to our second quarter of fiscal year 2009 opening condensed consolidated balance sheet and to the opening December 31, 2008 condensed consolidated balance sheet (in thousands):

	June 30, 2009			December 31, 2008
Decrease in intangible assets, net	$	(3,320	)	$	(3,141	)
Increase in accumulated deficit		(3,320	)		(3,141	)

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The impact on accumulated deficit by quarter which is caused by an increase in cost of product sales and a corresponding increase in loss from operations and net loss, is comprised of the following amounts (in thousands):

	Quarter Ended
	(Unaudited)
	March 31			June 30			Sept 30			Dec 31			Total
Quarter Ended June 30, 2009 Beginning Balance Adjustment:													$	(3,320	)
Increase in loss from operations, net loss and increase in cost of product sales:
Year Ended 2009	$	(179	)	$	—		$	—		$	—		$	(179	)
Year Ended 2008		(168	)		(169	)		(169	)		(168	)		(674	)
Year Ended 2007		(171	)		(168	)		(169	)		(169	)		(677	)
Prior to Year Ended 2007		—			—			—			—			(1,790	)
													$	(3,320	)

Net loss per share did not change for the three and six months ended June 30, 2008 due to the patent license amortization error. In addition, net cash provided by operations in the condensed consolidated statement of cash flows for the six months ended June 30, 2008 did not change because the increase in the net loss of $338,000 was offset by the increase of $338,000 in the amortization of intangible assets.

As the errors were not material to prior year financial statements when evaluated under the “rollover” approach but were material to the 2009 condensed consolidated financial statements when evaluated under the “iron curtain” method, we will correct previously issued financial statements prospectively, that is, the next time those financial statements are required to be presented. The financial statements corrected prospectively include those included in this Form 10-Q, and will include the September 30, 2009 Form 10-Q, and the 2009 Form 10-K when they are filed.

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ITEM 2. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

Forward-Looking Statements

This Quarterly Report on Form 10-Q, including this Management’s Discussion and Analysis of Financial Condition and Results of Operations, contains forward-looking statements that are based upon current expectations. These statements are forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. In some cases, you can identify forward-looking statements by terminology such as “may”, “will”, “should”, “expect”, “plan”, “anticipate”, “believe”, “estimate”, “intend”, “potential” or “continue” or the negative of these terms or other comparable terminology. Forward-looking statements are based upon current expectations that involve risks and uncertainties. Our actual results and the timing of events could differ materially from those anticipated in our forward-looking statements as a result of many factors, including, but not limited to, the following: the adverse impact of the significant global economic downturn on our target markets and our business; continued market acceptance of our healthcare associated infection products; changes in the protocols, best practices or level of testing for healthcare associated infections; development and manufacturing problems; the need for additional intellectual property licenses for new tests and other products and the terms of such licenses; our ability to successfully sell additional products in the Clinical market; lengthy sales cycles in certain markets; the performance and market acceptance of our new products; our ability to obtain regulatory approvals and introduce new products into the Clinical market; the level of testing at existing clinical customer sites; the mix of products sold, which can affect gross margins; our reliance on distributors to market, sell and support our products; the occurrence of unforeseen expenditures, asset impairments, acquisitions or other transactions; our ability to integrate the businesses, technologies, operations and personnel of acquired companies; the scope and timing of actual United States Postal Service (“USPS”) funding of the Biohazard Detection System (“BDS”) in its current configuration; the rate of environmental testing using the BDS conducted by the USPS, which will affect the amount of consumable products sold; our success in increasing our direct sales and the effectiveness of our sales personnel; the impact of competitive products and pricing; our ability to manage geographically-dispersed operations; our ability to continue to realize manufacturing efficiencies, which are an important factor in improving gross margins; underlying market conditions worldwide; and the other risks set forth under “Risk Factors” and elsewhere in this report. We assume no obligation to update any of the forward-looking statements after the date of this report or to conform these forward-looking statements to actual results.

OVERVIEW

We are a broad-based molecular diagnostics company that develops, manufactures, and markets fully-integrated systems for testing in the Clinical market, as well as for application in our legacy Biothreat, Industrial and Partner markets. Our systems enable rapid, sophisticated molecular testing for organisms and genetic-based diseases by automating otherwise complex manual laboratory procedures. Molecular testing historically has involved a number of complicated and time-intensive steps, including sample preparation, DNA amplification and detection. Our easy-to-use systems integrate these steps and analyze complex biological samples in our proprietary test cartridges. We are currently the only company to have obtained Clinical Laboratory Improvement Amendments (“CLIA”) moderate complexity categorization for an amplified molecular test system and associated specific infectious disease tests on the market in the United States. Our efforts are principally focused on those Clinical applications where rapid and accurate testing is particularly important, such as identifying infectious diseases and cancer.

Our two principal systems are the GeneXpert and SmartCycler systems. The GeneXpert system, our primary offering in the Clinical market, integrates sample preparation in addition to DNA amplification and detection. The GeneXpert system is designed for a broad range of user types ranging from reference laboratories and hospital central laboratories to satellite testing locations, such as emergency departments and intensive care units within hospitals and doctors’ offices. The GeneXpert system is also our main system in the Biothreat market. The SmartCycler system integrates DNA amplification and detection to allow rapid analysis of a sample.

The GeneXpert system represents a paradigm shift in molecular diagnostics in terms of ease-of-use and flexibility, producing accurate results in a timely manner with minimal risk of contamination. Our GeneXpert system can provide rapid results with superior test specificity and sensitivity over comparable systems on the market today that are integrated but have open architectures.

We currently have available a broad and expanding menu of tests and reagents for use on our systems. Our reagents and tests are marketed along with our systems on a worldwide basis.

Sales Channels

Sales for products within our specific markets are conducted through both direct sales and indirect distribution channels worldwide. Clinical market sales in the United States and the United Kingdom are handled primarily through our direct sales force, while sales in all other markets are handled primarily through distributors. As international Clinical markets continue to develop, we expect to expand our direct sales efforts. Our marketing programs are managed on a direct basis.

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Revenues

Currently, we derive our revenues primarily from the sales of our two systems and associated reagents and disposables in the Clinical, Biothreat, Industrial and Partner markets, and to a lesser extent from contract and government sponsored research.

Research and Development

The principal objective of our research and development program is to develop high-value clinical diagnostic products for the GeneXpert system. We focus our efforts on four main areas: a) assay development efforts to design, optimize, and produce specific tests that leverage the systems and chemistry we have developed, b) target discovery research to identify novel micro RNA targets to be used in the development of future assays, c) chemistry research to develop innovative and proprietary methods to design and synthesize oligonucleotide primers, probes and dyes to optimize the speed, performance and ease-of-use of our assays and d) engineering efforts to extend the multiplexing capabilities of our systems and to develop new low and high throughput systems.

CRITICAL ACCOUNTING POLICIES, ESTIMATES AND ASSUMPTIONS

Management believes that there have been no significant changes during the six months ended June 30, 2009 to the items that we disclosed as our critical accounting policies and estimates in Management’s Discussion and Analysis of Financial Condition and Results of Operation in our 2008 Annual Report on Form 10-K filed with the Securities and Exchange Commission. For a description of those critical accounting policies, please refer to our 2008 Annual Report on Form 10-K.

RESULTS OF OPERATIONS

Comparison of the Three and Six Months Ended June 30, 2009 and 2008

Revenues

	Three Months Ended June 30,						Six Months Ended June 30,
	2009		2008		% Change		2009		2008		% Change
	(In thousands)						(In thousands)
Revenues:
System sales	$	8,911	$	12,423	-28	%	$	16,820	$	26,747	-37	%
Reagent and disposable sales		30,649		26,530	16	%		59,328		54,126	10	%
Total product sales		39,560		38,953	2	%		76,148		80,873	-6	%
Other revenue		1,461		3,097	-53	%		3,640		6,010	-39	%
Total revenues	$	41,021	$	42,050	-2	%	$	79,788	$	86,883	-8	%

We operate in four market areas: Clinical, Industrial, Biothreat and Partner. The following table illustrates product sales in the four market areas as a percentage of total product sales:

	Three Months Ended June 30,						Six Months Ended June 30,
	2009		2008		% Change		2009		2008		% Change
	(In thousands)						(In thousands)
Product sales by market:
Clinical Systems	$	5,669	$	6,603	-14	%	$	10,442	$	13,648	-23	%
Clinical Reagents		20,993		13,665	54	%		40,004		24,268	65	%
Total Clinical		26,662		20,268	32	%		50,446		37,916	33	%
Industrial		4,329		3,695	17	%		8,024		7,299	10	%
Biothreat		7,753		9,411	-18	%		15,679		21,973	-29	%
Partner		816		5,579	-85	%		1,999		13,685	-85	%
Total product sales	$	39,560	$	38,953	2	%	$	76,148	$	80,873	-6	%

Total product sales increased 2% to $39.6 million in the second quarter of 2009 from $39.0 million in the second quarter of 2008, primarily due to an increase in Clinical sales of $6.4 million, or 32%, offset by a decrease in our legacy Biothreat and

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Partner markets of $6.4 million. Clinical Reagents grew $7.3 million or 54%, driven primarily by an increase in sales of our healthcare associated infection (“HAI”) tests, offset by a $0.9 million or 14% decrease in Clinical Systems product sales, as customers have continued to be constrained by budgets due to the effect of the challenging economic environment on capital purchase decisions. The decrease of $4.8 million or 85% in Partner product sales was due to the expiration of our contract with Becton Dickinson in the fourth quarter of 2008 and the cancellation of certain contracted purchases by Roche during 2008. In the Biothreat market, product sales decreased $1.7 million from the second quarter of 2008 compared to the same period in 2009, primarily due to reduced anthrax test cartridge sales to Northrop Grumman/USPS.

For the six months ended June 30, 2009, total product sales were $76.1 million, a decrease of 6% from $80.9 million for the six months ended June 30, 2008. The decrease was a result of a decline in sales in our legacy Biothreat and Partner markets of $18.0 million, offset by an increase in Clinical sales of $12.5 million or 33%. Clinical Reagents grew $15.7 million or 65%, driven primarily by an increase in sales of our HAI tests, offset by a $3.2 million or 23% decrease in Clinical Systems product sales, as customers have continued to be constrained by the effect of the challenging economic environment on capital purchase decisions. The decrease of $11.7 million or 85% in Partner product sales was due to the expiration of our contract with Becton Dickinson in the fourth quarter of 2008 and the cancellation of certain contracted purchases by Roche during 2008. In the Biothreat market, product sales decreased $6.3 million or 29% primarily due to reduced anthrax test cartridge sales to Northrop Grumman/USPS.

We expect our Clinical product sales to continue to increase during the remainder of 2009 with the continued expansion of the HAI market and our new products. We expect that our Partner product sales will not change significantly from the second quarter of 2009 throughout the remainder of 2009. We expect our Biothreat sales to further decrease during the remainder of 2009, due to both the quarterly linearity of purchases by the USPS this year and our expectation that the USPS will purchase the contractual minimum level of product for the rest of the year.

The following table provides a breakdown of our product sales by geographic regions (in thousands):

	Three Months Ended June 30,						Six Months Ended June 30,
	2009		2008		% Change		2009		2008		% Change
Product Sales Geographic information:
North America
Clinical	$	20,145	$	15,498	30	%	$	38,513	$	28,310	36	%
Other		11,196		14,211	-21	%		22,025		32,823	-33	%
Total North America		31,341		29,709	5	%		60,538		61,133	-1	%
International
Clinical	$	6,517	$	4,770	37	%	$	11,933	$	9,606	24	%
Other		1,702		4,474	-62	%		3,677		10,134	-64	%
Total International		8,219		9,244	-11	%		15,610		19,740	-21	%
Total product sales	$	39,560	$	38,953	2	%	$	76,148	$	80,873	-6	%

Product sales in North America increased $1.6 million, or 5%, from $29.7 million in the second quarter of 2008 to $31.3 million in the second quarter of 2009. The increase in North America product sales was primarily driven by a $4.6 million increase in Clinical sales due to higher sales of HAI tests, offset by a $1.7 million decline in anthrax test cartridge sales to Northrop Grumman/USPS in the Biothreat market, as well as lower Partner sales. In the Clinical market, increases in reagents sales more than offset a decline in systems sales. Internationally, which primarily represents sales in Europe, product sales decreased $1.0 million, or 11%, from $9.2 million in the second quarter of 2008 to $8.2 million in the second quarter of 2009. The decrease in international sales is related to a $3.0 million decrease in Partner sales due to the expiration of our contract with Becton Dickinson in the fourth quarter of 2008 and the cancellation of certain contracted purchases by Roche during 2008. International Clinical sales grew by $1.7 million.

Product sales in North America decreased $0.6 million, or 1%, from $61.1 million for the six months ended June 30, 2008 to $60.5 million for the six months ended June 30, 2009. The decrease in North America product sales was primarily driven by a $6.3 million decline in anthrax test cartridge sales to Northrop Grumman/USPS in the Biothreat market and lower Partner sales. The decrease is partially offset by a $10.2 million increase in Clinical sales, due to higher reagents sales offsetting lower systems sales. Internationally, which primarily represents sales in Europe, product sales decreased $4.1 million, or 21%, from $19.7 million in the six months ended June 30, 2008 to $15.6 million for the six months ended 2009. The decrease in international sales is mainly due to a $7.0 million decrease in Partner sales for the same reason noted above. International Clinical sales grew by $2.3 million.

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No single country outside of the United States represented more than 10% of our total revenues in any period presented.

Other revenue of $1.5 million for the three months ended June 30, 2009 decreased 53% from $3.0 million for the same period in 2008. For the six months ended June 30, 2009, other revenue decreased 39% from $6.0 million for the six months ended June 30, 2008 to $3.6 million. The decrease in each period was primarily due to a decrease in our program associated with the development of our test for genetic polymorphisms in clotting factors II and V as well as the termination of the Centers for Disease Control program in the third quarter of 2007 for which revenue continued into the first half of 2008. We expect that our quarterly Other revenue will decrease during the remainder of 2009 as certain of our collaboration projects reach transition levels in their lifecycles.

Costs and Operating Expenses

	Three Months Ended June 30,						Six Months Ended June 30,
	2009		2008		% Change		2009		2008		% Change
	(In thousands)						(In thousands)
			As Restated (1)						As Restated (1)
Costs and operating expenses:
Cost of product sales	$	23,250	$	23,039	1	%	$	43,940	$	46,193	-5	%
Collaboration profit sharing		2,612		2,777	-6	%		5,241		6,510	-19	%
Research and development		10,315		10,964	-6	%		20,653		20,862	-1	%
Sales and marketing		6,917		7,434	-7	%		13,729		14,375	-4	%
General and administrative		5,340		5,518	-3	%		10,609		10,265	3	%
Restructuring charge		—		—	100	%		747		—	100	%
Total costs and operating expenses	$	48,434	$	49,732	-3	%	$	94,919	$	98,205	-3	%

(1) See Note 11, “Restatement of Condensed Consolidated Financial Statements” in Notes to Condensed Consolidated Financial Statements.

Cost of Product Sales

Cost of product sales consists of raw materials, direct labor and stock-based compensation expense, manufacturing overhead, facility costs and warranty costs. Cost of product sales also includes royalties on product sales and amortization of intangible assets related to technology licenses and intangibles acquired in the purchase of Sangtec. As a result of the increased product sales in the second quarter of 2009 from the second quarter of 2008 discussed above, cost of product sales increased 1% to $23.2 million for the second quarter of 2009 compared to $23.0 million for the second quarter of 2008. Our product gross margin percentage was 41% for both the second quarter of 2009 and 2008. For the six months ended June 30, 2009 and 2008, cost of product sales decreased 5% to $43.9 million from $46.2 million as a result of the decreased product sales discussed above. Our product margin percentage was 42% for the six months ended June 30, 2009 compared to 43% for the six months ended June 30, 2008. The slight decrease in product gross margin percentage in the six months ended June 30, 2009 versus the same period in 2008 was primarily due to an increase in license fee amortization expense from additional licenses and under-absorption of overhead in our European manufacturing facility that manufactures product for Roche, which cancelled certain contract purchases in 2008.

Collaboration Profit Sharing

Collaboration profit sharing represents the amount that we pay to ABI (now Life Technologies Corporation) under our collaboration agreement to develop reagents for use in the USPS BDS program. Under the agreement, computed gross margin on anthrax cartridge sales are shared equally between the two parties. Collaboration profit sharing expense was $2.6 million and $2.8 million for the second quarter of 2009 and 2008, respectively, and $5.2 million and $6.5 million for the six months of 2009 and 2008, respectively. The decreases in collaboration profit sharing for the second quarter of 2009 as compared to the second quarter of 2008 and the first six months of 2009 as compared to the first six months of 2009 were the result of decreased anthrax cartridge sales under the USPS BDS program. This expense will remain approximately proportional to the sales of anthrax cartridges under the USPS BDS program, which we expect will decrease throughout the remainder of 2009.

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Research and Development Expenses

Research and development expenses consist of salaries and employee-related expenses, which include stock-based compensation, clinical trials, research and development materials, facility costs and depreciation. Research and development expenses decreased 6% to $10.3 million for the second quarter of 2009 from $11.0 million for the second quarter of 2008. The decrease in research and development expenses of $0.7 million is primarily due to a $0.3 million decrease in research and development supplies and offset by a $0.1 million decrease in clinical trial costs. For the six months ended June 30, 2009, research and development expenses decreased 1% to $20.7 million as compared to $20.9 million for the six months ended June 30, 2008. The decrease in research and development expenses of $0.2 million is primarily due to a $0.7 million decrease in research and development supplies, offset by a $0.3 million increase in employee related expense and a $0.1 million increase in clinical trial costs. We expect that our research and development expenses will decrease as a percentage of total revenues throughout the remainder of 2009.

Sales and Marketing Expenses

Sales and marketing expenses consist primarily of salaries and employee-related expenses, which include commissions and stock-based compensation, travel, facility-related costs and marketing and promotion expenses. Sales and marketing expenses decreased 7% to $6.9 million for the second quarter of 2009 from $7.4 million for the second quarter of 2008. The decrease in sales and marketing expenses is primarily due to a $0.2 million decrease in contractor costs and a $0.2 million decrease in advertising expense. Sales and marketing expenses decreased 4% to $13.7 million for the six months ended June 30, 2009 from $14.4 million for the six months ended June 30, 2008. The decrease in sales and marketing expenses is primarily due to a $0.3 million decrease in contractor costs, a $0.3 million decrease in advertising expense and a $0.2 million decrease in travel expense. We expect our sales and marketing expenses will increase modestly throughout the remainder of 2009 as we continue to expand our efforts in the Clinical market, with particular emphasis on pursuing the market opportunities for our GeneXpert products.

General and Administrative Expenses

General and administrative expenses consist primarily of salaries and employee-related expenses, which include stock-based compensation, travel, facility costs, legal, accounting and other professional fees. General and administrative expenses decreased 3% to $5.3 million for the second quarter of 2009 from $5.5 million for the second quarter of 2008. The decrease is primarily due to a $0.4 million decrease in other professional expenses and a $0.2 million decrease in contracting costs. The decrease was partially offset by a $0.5 million increase in salaries and employee-related expenses. General and administrative expenses increased 3% to $10.6 million for the six months ended June 30, 2009 from $10.3 million for the six months ended June 30, 2009. The increase is primarily due to a $1.5 million increase in salaries and employee-related expenses, inclusive of a $0.4 million increase in stock-based compensation, offset by a $0.6 million decrease of contractor costs and a $0.5 million decrease in other professional expenses. We expect our general and administrative expenses to decline as a percentage of total revenues throughout the remainder of 2009.

Restructuring Charge

During the first quarter of 2009, we eliminated 47 positions that impacted employees, contractors and replacement positions, which resulted in $0.7 million of restructuring expense, mainly related to severance. As of June 30, 2009, we have no material outstanding restructuring expenses to be paid.

Other Income (Expense), Net

	Three Months Ended June 30,								Six Months Ended June 30,
	2009			2008			% Change		2009			2008			% Change
	(In thousands)								(In thousands)
Other income (expense), net:
Interest income	$	116		$	258		-55	%	$	248		$	798		-69	%
Interest expense		(72	)		(1	)	7100	%		(148	)		(2	)	7300	%
Foreign currency exchange gain and other		415			(66	)	-729	%		431			677		-36	%
Total other income (expense), net	$	459		$	191		140	%	$	531		$	1,473		-64	%

Other income (expense), net consists of interest income, interest expense and foreign currency exchange gain, net and other. Interest income decreased to $0.1 million for the second quarter of 2009 from $0.3 million for the second quarter of 2008. Interest income decreased to $0.2 million for the six months ended June 30, 2009 from $0.8 million for the six months ended June 30, 2009. The decreases are primarily due to lower interest rates in 2009 as compared to 2008. The interest expense increase of $0.1 million for both the three and six months ended June 30, 2009 compared to the three and six months ended June 30, 2008 is primarily due to

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interest expense related to our UBS loan entered into during the fourth quarter of 2008. Foreign currency exchange gain and other increased $0.5 million for the three months ended June 30, 2009 as compared to the three months ended June 30, 2008, primarily due to the auction rate securities gain of $0.5 million. Foreign currency exchange gain and other decreased $0.3 million for the six months ended June 30, 2009 as compared to the six months ended June 30, 2008 as a result of foreign currency exchange losses in 2008 prior to the implementation of our foreign currency hedge program which we initiated during the fourth quarter of 2008 to limit our currency risk exposure.

LIQUIDITY AND CAPITAL RESOURCES

Cash and Cash Flow

	Six Months Ended June 30,
	2009			2008			Increase/ (Decrease)
	(In thousands)
Net cash provided by operating activities	$	1,724		$	4,564		$	(2,840	)
Net cash used in investing activities		(2,931	)		(5,520	)		2,589
Net cash provided by financing activities		2,343			9,329			(6,986	)

As of June 30, 2009, we had $24.7 million in cash and cash equivalents. The $1.2 million increase in total cash, cash equivalents and short-term investments for the six months ended June 30, 2009 consisted primarily of $2.3 million provided by financing activities and $1.7 million provided by operating activities, offset by $2.9 million used in investing activities.

Net cash provided by operating activities was $1.7 million and $4.6 million for the six months ended June 30, 2009 and June 30, 2008, respectively. The net cash provided by operating activities was primarily comprised of net loss plus the net effect of non-cash expenses. Non-cash expenses are comprised of stock-based compensation, unrealized loss on put option, depreciation and amortization expenses and prepaid compensation expense, offset by an unrealized gain on auction rate securities and deferred rent expense. The primary working capital sources of cash were increases in accounts payable and other current liabilities, and decreases in prepaid expenses, other current assets and accounts receivable. The primary working capital uses of cash were increases in inventory and other non-current assets, and decreases in accrued compensation and deferred revenue.

Net cash used in investing activities was $2.9 million and $5.5 million for the six months ended June 30, 2009 and June 30, 2008, respectively. For the six months ended June 30, 2009, net cash used in investing activities consisted of payments for technology licenses, net capital expenditures, and the cost of an acquisition offset by a transfer of restricted cash to unrestricted cash. For the six months ended June 30, 2008, net cash used in investing activities consisted of net capital expenditures offset by proceeds from maturities of marketable securities. The change in net cash used in investing activities for the six months ended June 30, 2009 from the same period ended June 30, 2008 is primarily due to a decrease in capital expenditures offset by a decrease in proceeds from maturities of marketable securities.

Net cash provided by financing activities was $2.3 million and $9.3 million for the six months ended June 30, 2009 and 2008, respectively. The change is primarily due to the decrease in net proceeds from the issuance of common shares under our employee stock purchase plan and exercise of stock options.

At June 30, 2009, we had $25.0 million invested in auction rate securities at cost and $22.0 million at fair value, all of which have failed to settle at auction since March 2008. At June 30, 2009, all but three of our auction rate securities continue to carry at least an AAA rating by at least one of the major rating agencies. Our auction rate securities consist of investments that are backed by pools of student loans, which are principally guaranteed by the Federal Family Educational Loan Program (“FFELP”), or insured.

In October 2008, UBS offered us an option to sell the auction rate securities held by us back to UBS at par value beginning June 30, 2010 until July 2, 2012 and with an offer to provide “no net cost” loans to us up to 75% of the fair value of the auction rate securities. On November 10, 2008, we accepted this offer and borrowed $14.7 million on the line of credit. In accepting the settlement arrangement, we also granted UBS the right to sell our auction rate securities at par at any time up until the expiration date of the rights and released UBS from any claims related to the marketing and sale of auction rate securities, other than claims for consequential damages. The put option with fair value of $2.9 million is a separate freestanding instrument and is accounted for separately from our auction rate securities investment. We intend to exercise our option and sell the auction rate securities back at par beginning June 30, 2010 through July 2, 2012, depending on market conditions.

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In the first six months of 2009, we recorded a gain to other income (expense) of $6.9 million increased the value of our auction rate securities investments classified as trading securities, offset by a loss of $6.5 million of the estimated fair value of the put option. We do not believe that the auction failures and our inability to liquidate these investments for some period of time will have any material impact on our ability to fund our operating requirements, capital expenditures, acquisitions, if any, or other business requirements.

In May 2009, we extended one of our long-term operating lease obligations for approximately 76,000 square feet of office and laboratory space in Sunnyvale, California from an expiration date of March 2012 to March 2015. Rent expense for all operating leases for both the three months ended June 30, 2009 and 2008 was $0.9 million, and $1.7 million and $1.6 million for the six months ended June 30, 2009 and 2008, respectively. The impact on future commitments is included in the minimum annual rental commitments under facilities operating leases table in Note 8 of the Notes to Condensed Consolidated Financial Statements.

Off-Balance-Sheet Arrangements

As of June 30, 2009, we did not have any off-balance-sheet arrangements, as defined in Item 303(a)(4)(ii) of Regulation S-K promulgated under the Securities Act of 1933.

Financial Condition Outlook

We plan to continue to make expenditures to expand our manufacturing capacity and to support our activities in sales and marketing and research and development. We plan to continue to support our working capital needs and anticipate that our existing cash resources will enable us to maintain currently planned operations. This expectation is based on our current and long-term operating plan and may change as a result of many factors, including our future capital requirements and our ability to increase revenues and reduce expenses, which, in many instances, depend on a number of factors outside our control including the general decline in global economic conditions. For example, our future cash use will depend on, among other things, market acceptance of our products, the resources we devote to developing and supporting our products, continued progress of our research and development of potential products, the need to acquire licenses to new technology or to use our technology in new markets, expansion through acquisitions and the availability of other financing.

In the future, we may seek additional funds to support our strategic business needs and may seek to raise such additional funds through private or public sales of securities, strategic relationships, bank debt, lease financing arrangements, or other available means. If additional funds are raised through the issuance of equity or equity-related securities, stockholders may experience additional dilution, or such equity securities may have rights, preferences, or privileges senior to those of the holders of our common stock. If adequate funds are not available or are not available on acceptable terms to meet our business needs, our business may be harmed.

Please see Note 8 to our financial statements included herein for a description of certain changes to our commitments and contingencies.

ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

The primary objective of our investment activities is to preserve principal while at the same time maximizing the income we receive from our investments without significantly increasing risk. Our investments in interest-bearing assets are subject to interest rate risk. This means that a change in prevailing interest rates may cause the principal amount of the investment to fluctuate. For example, if we hold a security that was issued with a fixed interest rate at the then-prevailing rate and the prevailing interest rate later rises, the principal amount of our investment will probably decline. To minimize this risk, we maintain our interest-bearing portfolio, which consists of cash and cash equivalents, in money market funds. Due to the short-term nature of the investments, we believe we currently have no material exposure to interest rate risk arising from our investments. Therefore we have not included quantitative tabular disclosure in this Form 10-Q. As described above, we had $25.0 million invested in auction rate securities at cost, all of which have failed to settle at auction since March 2008. See “Liquidity and Capital Resources – Cash and Cash Flow” above for a description of our auction rate securities and settlement with UBS. We valued these securities using a discounted cash flow methodology. Significant inputs that went into the model were the credit quality of the issuer, the percentage and the types of guarantees, contractual maturity, the timing and probability of the auction succeeding or the security being called and discount factors. The assumptions used in preparing the discounted cash flow model include estimates of interest rates, timing and amount of cash flows and expected holding period of the auction rate securities and the put option. The assumptions are based on data available as of June 30, 2009 for interest rates, timing and amount of cash flows, credit and liquidity premiums, and expected holding periods of the ARS. These assumptions are volatile and subject to change as the underlying sources of these assumptions and market conditions change and could result in significant changes to the fair value of auction rate securities.

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We operate primarily in the United States and a majority of our revenue, cost, expense and capital purchasing activities for the six months ended June 30, 2009 were transacted in U.S. Dollars. As a corporation with international as well as domestic operations, we are exposed to changes in foreign exchange rates. These exposures may change over time and could have a material adverse impact on our financial results. As of June 30, 2009, we had two outstanding foreign exchange forward contracts which were recorded as a derivative asset within Prepaid expenses and other current assets with a fair value of approximately $0.1 million representing the estimated gain on those outstanding foreign currency exchange forward contracts as of June 30, 2009 and derivative liability within Accrued and other liabilities with a fair value of approximately $0.1 million representing the estimated loss on those outstanding foreign currency exchange forward contracts as of June 30, 2009. During the three and six months ended June 30, 2009, the effect of our hedging transactions, consisting entirely of foreign currency forward contracts, on our condensed consolidated statement of operations was a pre-tax loss of approximately $0.4 million and $0.3 million, respectively.

We will continue to use hedging programs in the future and may use currency forward contracts, currency options, and/or other derivative financial instruments commonly utilized to reduce financial market risks if it is determined that such hedging activities are appropriate to reduce risk.

ITEM 4. CONTROLS AND PROCEDURES

EVALUATION OF DISCLOSURE CONTROLS AND PROCEDURES

Regulations under the Securities Exchange Act of 1934 (the “Exchange Act”) require public companies, including our company, to maintain “disclosure controls and procedures”, which are defined to mean a company’s controls and other procedures that are designed to ensure that information required to be disclosed in the reports that it files or submits under the Exchange Act is accumulated and timely communicated to management, including our Chief Executive Officer and Chief Financial Officer, recorded, processed, summarized, and reported, within the time periods specified in the Securities and Exchange Commission’s rules and forms. Our Chief Executive Officer and our Chief Financial Officer, based on their evaluation of our disclosure controls and procedures as of the end of the period covered by of this report, concluded that our disclosure controls and procedures were effective for this purpose.

CHANGES IN INTERNAL CONTROL OVER FINANCIAL REPORTING

Regulations under the Exchange Act require public companies, including our company, to evaluate any change in our “internal control over financial reporting”, which is defined as a process to provide reasonable assurance regarding the reliability of financial reporting and preparation of financial statements for external purposes in accordance with accounting principles generally accepted in the United States. In connection with their evaluation of our disclosure controls and procedures as of the end of the period covered by this report, our Chief Executive Officer and Chief Financial Officer did not identify any change in our internal control over financial reporting during the six months ended June 30, 2009, that materially affected, or is reasonably likely to materially affect, our internal control over financial reporting.

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PART II — OTHER INFORMATION

ITEM 1. LEGAL PROCEEDINGS

We are not currently a party to any material legal proceedings.

ITEM 1A. RISK FACTORS

You should carefully consider the risks and uncertainties described below, together with all of the other information included in this Report, in considering our business and prospects. The risks and uncertainties described below are not the only ones facing us. Additional risks and uncertainties not presently known to us or that we currently deem immaterial also may impair our business operations. The occurrence of any of the following risks could harm our business, financial condition or results of operations.

We may not achieve profitability.

We have incurred operating losses in each period since our inception. We experienced net losses of approximately $22.1 million in 2007, $22.4 million in 2008 and $14.4 million for the first six months of 2009 and we do not anticipate that we will achieve profitability for 2009. As of June 30, 2009, we had an accumulated deficit of approximately $194.1 million. Our ability to become profitable will depend on our ability to continue to increase our revenues, which is subject to a number of factors including the uncertainty of the impact of the global economic slowdown on our customers, suppliers and partners, our ability to continue to successfully penetrate the Clinical market, our ability to successfully market the GeneXpert system and develop effective GeneXpert tests, continued growth in sales of our healthcare associated infection tests, the extent of our participation in the USPS BDS program and the operating parameters of the USPS BDS program, which will affect the rate of our consumable products sold, our ability to compete effectively against current and future competitors, and global economic and political conditions. Our ability to become profitable also depends on our expense levels and product gross margin, which are also influenced by a number of factors, including the resources we devote to developing and supporting our products, the continued progress of our research and development of potential products, the ability to gain FDA clearance for our products, our ability to improve manufacturing efficiencies, license fees or royalties we may be required to pay, our ability to integrate acquired businesses and technologies, acquisition-related costs and expenses and the potential need to acquire licenses to new technology or to use our technology in new markets, which could require us to pay unanticipated license fees and royalties in connection with these licenses. Our expansion efforts may prove more expensive than we currently anticipate, and we may not succeed in increasing our revenues to offset higher expenses. These expenses, among other things, may cause our net income and working capital to decrease. If we fail to grow our revenue and manage our expenses and improve our product gross margin, we may never achieve profitability. If we fail to do so, the market price of our common stock will likely decline.

The recent deterioration and current uncertainty in global economic conditions makes it particularly difficult to predict product demand and other related matters, and makes it more likely that our actual results could differ materially from expectations.

Our operations and performance depend on worldwide economic conditions, which have been adversely impacted by extreme disruption in the financial markets of the United States and other countries, and may remain depressed for the foreseeable future. These conditions make it difficult for our customers and potential customers to accurately forecast and plan future business activities, and has caused our customers and potential customers to slow or reduce spending. Furthermore, during challenging economic times, our customers have experienced and may continue to experience issues gaining timely access to sufficient credit, which could result in their unwillingness to purchase products or an impairment of their ability to make timely payments to us. If that were to continue to occur, we may experience decreased sales, be required to increase our allowance for doubtful accounts and our days sales outstanding would be negatively impacted. We cannot predict the timing, strength or duration of any economic slowdown or subsequent economic recovery, worldwide, in the United States or in our industry. These and other economic factors could have a material adverse effect on demand for our products and on our financial condition and operating results.

Our operating results may fluctuate significantly, particularly given adverse worldwide economic conditions, and any failure to meet financial expectations may result in a decline in our stock price.

Our quarterly operating results may fluctuate in the future as a result of many factors, such as those described elsewhere in this section, many of which are beyond our control. Because our revenue and operating results are difficult to predict, we believe that period-to-period comparisons of our results of operations are not a good indicator of our future performance. Our operating results may be affected by the inability of some of our customers to consummate anticipated purchases of our products, whether due to the global economic downturn, changes in internal priorities or, in the case of governmental customers, problems with the appropriations process and variability and timing of orders, changes in procedures or protocols with respect to testing or

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manufacturing inefficiencies. If revenue declines in a quarter, whether due to a delay in recognizing expected revenue, adverse economic conditions, and unexpected costs or otherwise, our results of operations will be harmed because many of our expenses are relatively fixed. In particular, research and development, sales and marketing and general and administrative expenses are not significantly affected by variations in revenue. If our quarterly operating results fail to meet or exceed the expectations of securities analysts or investors, our stock price could drop suddenly and significantly.

Our sales cycle can be lengthy, which can cause variability and unpredictability in our operating results.

The sales cycles for our systems products can be lengthy, particularly during the current economic downturn, which makes it more difficult for us to accurately forecast revenues in a given period, and may cause revenues and operating results to vary significantly from period to period. For example, sales of our products involving our corporate accounts within the Clinical market and those within the Industrial market often involve purchasing decisions by large public and private institutions, and any purchases can require many levels of pre-approval. In addition, certain Industrial sales may depend on these institutions receiving research grants from various federal agencies, which grants vary considerably from year to year in both amount and timing due to the political process. As a result, we may expend considerable resources on unsuccessful sales efforts or we may not be able to complete transactions on the schedule anticipated.

If we cannot successfully commercialize our products, our business could be harmed.

If our tests for use on our systems do not gain continued market acceptance, we will be unable to generate significant sales, which will prevent us from achieving profitability. While we have received FDA clearance for a number of tests, these products may not continue to experience increased sales. Many factors may affect the market acceptance and commercial success of our products, including:

• timely expansion of our menu of tests and reagents;

• the results of clinical trials needed to support any regulatory approvals of our tests;

• our ability to obtain requisite FDA or other regulatory clearances or approvals for our tests under development on a timely basis;

• demand for the tests and reagents we introduce;

• the timing of market entry for various tests for the GeneXpert and the SmartCycler systems;

• our ability to convince our potential customers of the advantages and economic value of our systems and tests over competing technologies and products;

• the breadth of our test menu relative to competitors;

• changes to policies, procedures or what are considered best practices in clinical diagnostics, including practices for detecting and preventing healthcare associated infections;

• the extent and success of our marketing and sales efforts;

• level of reimbursement for our products by third-party payers; and

• publicity concerning our systems and tests.

In particular, we believe that the success of our business will depend in large part on our ability to continue to increase sales of our Xpert tests and our ability to introduce additional tests for the Clinical market. We believe that successfully expanding our business in the Clinical market is critical to our long-term goals and success. We have limited ability to forecast future demand for our products in this market. In addition, we have committed substantial funds to licenses that are required for us to compete in the Clinical market. If we cannot successfully penetrate the Clinical market to fully exploit these licenses, these investments may not yield significant returns, which could harm our business.

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The regulatory approval process is expensive, time-consuming, and uncertain and may prevent us from obtaining required approvals for the commercialization of some of our products.

In the Clinical market, our products are regulated as medical device products by the FDA and comparable agencies of other countries. In particular, FDA regulations govern activities such as product development, product testing, product labeling, product storage, premarket clearance or approval, manufacturing, advertising, promotion, product sales, reporting of certain product failures and distribution. Some of our products, depending on their intended use, will require premarket approval (“PMA”) or 510(k) clearance from the FDA prior to marketing. The 510(k) clearance process usually takes from three to four months from submission but can take longer. The PMA process is much more costly, lengthy and uncertain and generally takes from six months to one year or longer from submission. Clinical trials are generally required to support both PMA and 510(k) submissions. Certain of our products for use on our GeneXpert and SmartCycler systems, when used for clinical purposes, may require PMA, and all such tests will most likely, at a minimum, require 510(k) clearance. We are planning clinical trials for other proposed products. Clinical trials are expensive and time-consuming. In addition, the commencement or completion of any clinical trials may be delayed or halted for any number of reasons, including product performance, changes in intended use, changes in medical practice and the opinion of evaluator Institutional Review Boards.

Failure to comply with the applicable requirements can result in, among other things, warning letters, administrative or judicially imposed sanctions such as injunctions, civil penalties, recall or seizure of products, total or partial suspension of production, refusal to grant premarket clearance or PMA for devices, withdrawal of marketing clearances or approvals, or criminal prosecution. With regard to future products for which we seek 510(k) clearance or PMA from the FDA, any failure or material delay to obtain such clearance or approval could harm our business. If the FDA were to disagree with our regulatory assessment and conclude that approval or clearance is necessary to market the products, we could be forced to cease marketing the products and seek approval or clearance. With regard to those future products for which we will seek 510(k) clearance or PMA from the FDA, any failure or material delay to obtain such clearance or approval could harm our business. In addition, it is possible that the current regulatory framework could change or additional regulations could arise at any stage during our product development or marketing, which may adversely affect our ability to obtain or maintain approval of our products and could harm our business.

Our manufacturing facilities located in Sunnyvale, California, Bothell, Washington and Bromma, Sweden, where we assemble and produce the GeneXpert and SmartCycler systems, cartridges and other molecular diagnostic kits and reagents, are subject to periodic regulatory inspections by the FDA and other federal and state and foreign regulatory agencies. For example, these facilities are subject to Quality System Regulations (“QSR”) of the FDA and are subject to annual inspection and licensing by the States of California and Washington and European regulatory agencies. If we fail to maintain these facilities in accordance with the QSR requirements, international quality standards or other regulatory requirements, our manufacturing process could be suspended or terminated, which would prevent us from being able to provide products to our customers in a timely fashion and therefore harm our business.

We rely on licenses of key technology from third parties and may require additional licenses for many of our new product candidates.

We rely on third-party licenses to be able to sell many of our products, and we could lose these third-party licenses for a number of reasons, including, for example, early terminations of such agreements due to breaches or alleged breaches by either party to the agreement. If we are unable to enter into a new agreement for licensed technologies, either on terms that are acceptable to us or at all, we may be unable to sell some of our products or access some geographic or industry markets. We also need to introduce new products and product features in order to market our products to a broader customer base and grow our revenues, and many new products and product features could require us to obtain additional licenses and pay additional license fees and royalties. Furthermore, for some markets, we intend to manufacture reagents and tests for use on our systems. We believe that manufacturing reagents and developing tests for our systems is important to our business and growth prospects but may require additional licenses, which may not be available on commercially reasonable terms or at all. Our ability to develop, manufacture and sell products, and our strategic plans and growth, could be impaired if we are unable to obtain these licenses or if these licenses are terminated or expire and cannot be renewed. We may not be able to obtain or renew licenses for a given product or product feature or for some reagents on commercially reasonable terms, if at all. Furthermore, some of our competitors have rights to technologies and reagents that we do not have which may put us at a competitive disadvantage in certain circumstances and could adversely affect our performance.

Our participation in the USPS BDS program may not result in predictable revenues in the future.

Our participation in the USPS BDS program involves significant uncertainties related to governmental decision-making and timing of deployment and is highly sensitive to changes in national priorities and budgets. Budgetary pressures may result in reduced allocations to projects such as the BDS program, sometimes without advance notice. We cannot be certain that actual funding and operating parameters, or product purchases, will occur at currently expected levels or in the currently expected timeframe.

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We may face risks associated with acquisitions of companies, products and technologies, and our business could be harmed if we are unable to address these risks.

If we are presented with appropriate opportunities, we intend to acquire or make other investments in complementary companies, products or technologies. We may not realize the anticipated benefit of any acquisition or investment. We will likely face risks, uncertainties and disruptions associated with the integration process, including difficulties in the integration of the operations and services of an acquired company, integration of acquired technology with our products, diversion of our management’s attention from other business concerns, the potential loss of key employees or customers of the acquired businesses and impairment charges if future acquisitions are not as successful as we originally anticipate. If we fail to successfully integrate other companies, products or technologies that we acquire, our business could be harmed. Furthermore, we may have to incur debt or issue equity securities to pay for any additional future acquisitions or investments, the issuance of which could be dilutive to our existing shareholders. In addition, our operating results may suffer because of acquisition-related costs or amortization expenses or charges relating to acquired intangible assets.

If we are unable to manufacture our products in sufficient quantities and in a timely manner, our operating results will be harmed and our ability to generate revenue could be diminished.

Our revenues and other operating results will depend in large part on our ability to manufacture and assemble our products in sufficient quantities and in a timely manner. Any interruptions we experience in the manufacturing or shipping of our products could delay our ability to recognize revenues in a particular quarter. Manufacturing problems can and do arise, and as demand for our products increases, any such problems could have an increasingly significant impact on our operating results. For example, during the second quarter of 2008, we experienced a manufacturing issue with respect to our cartridges, which caused us to experience increased costs and negatively affected our gross margin for that period. In the past, we have experienced problems and delays in production that have impacted our product yield and caused delays in our ability to ship finished products, and we may experience such delays in the future. We may not be able to react quickly enough to ship products and recognize anticipated revenues for a given period if we experience significant delays in the manufacturing process. In addition, we must maintain sufficient production capacity in order to minimize such delays, which carries fixed costs that we may not be able to offset if orders slow, which would adversely affect our operating margins. If we are unable to manufacture our products consistently, in sufficient quantities, and on a timely basis, our revenues from product sales, gross margins and our other operating results will be materially and adversely affected.

If certain single source suppliers fail to deliver key product components in a timely manner, our manufacturing ability would be impaired and our product sales could suffer.

We depend on certain single source suppliers that supply some of the components used in the manufacture of our systems and our disposable reaction tubes and cartridges. If we need alternative sources for key component parts for any reason, these component parts may not be immediately available to us. If alternative suppliers are not immediately available, we will have to identify and qualify alternative suppliers, and production of these components may be delayed. We may not be able to find an adequate alternative supplier in a reasonable time period or on commercially acceptable terms, if at all. Shipments of affected products have been limited or delayed as a result of such problems in the past, and similar problems could occur in the future. In addition, many companies are experiencing financial difficulties as a result of the global economic slowdown. We cannot assure you that our suppliers will not be adversely affected by these conditions or that they will be able to continue to provide us with the components we need. Our inability to obtain our key source supplies for the manufacture of our products may require us to delay shipments of products, harm customer relationships or force us to curtail or cease operations.

If certain of our products fail to obtain an adequate level of reimbursement from third-party payers, our ability to sell products in the Clinical market would be harmed.

Our ability to sell our products in the Clinical market will depend in part on the extent to which reimbursement for tests using our products will be available from government health administration authorities, private health coverage insurers, managed care organizations, and other organizations. There are efforts by governmental and third-party payers to contain or reduce the costs of health care through various means, and the continuous growth of managed care, together with efforts to reform the health care delivery system in the United States and Europe, has increased pressure on health care providers and participants in the health care industry to reduce costs. Consolidation among health care providers and other participants in the healthcare industry has resulted in fewer, more powerful groups, whose purchasing power gives them cost containment leverage. Additionally, third-party payers are increasingly challenging the price of medical products and services. If purchasers or users of our products are not able to obtain adequate reimbursement for the cost of using our products, they may forego or reduce their use. Significant uncertainty exists as to the reimbursement status of newly approved health care products and whether adequate third-party coverage will be available.

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If our competitors and potential competitors develop superior products and technologies, our competitive position and results of operations would suffer.

We face intense competition from a number of companies that offer products in our target markets, some of which have substantially greater financial resources and larger, more established marketing, sales and service organizations than we do. These competitors include:

• companies developing and marketing sequence detection systems for industrial research products;

• diagnostic and pharmaceutical companies;

• companies developing drug discovery technologies; and

• companies developing or offering biothreat detection technologies.

Several companies provide systems and reagents for DNA amplification or detection. ABI (now Life Technologies Corporation) and Roche sell systems integrating DNA amplification and detection (sequence detection systems) to the commercial market. Roche, Abbott Laboratories, BDC, Qiagen, Celera and GenProbe sell sequence detection systems, some with separate robotic batch DNA purification systems and sell reagents to the Clinical market. Other companies, including Siemens, Hologic, and bioMerieux, offer molecular tests.

If our products do not perform as expected or the reliability of the technology on which our products are based is questioned, we could experience lost revenue, delayed or reduced market acceptance of our products, increased costs and damage to our reputation.

Our success depends on the market’s confidence that we can provide reliable, high-quality molecular test systems. We believe that customers in our target markets are likely to be particularly sensitive to product defects and errors. Our reputation and the public image of our products or technologies may be impaired if our products fail to perform as expected or our products are perceived as difficult to use. Despite testing, defects or errors could occur in our products or technologies. Furthermore, with respect to the BDS program, our products are incorporated into larger systems that are built and delivered by others; we cannot control many aspects of the final system.

In the future, if our products experience a material defect or error, this could result in loss or delay of revenues, delayed market acceptance, damaged reputation, diversion of development resources, legal claims, increased insurance costs or increased service and warranty costs, any of which could harm our business. Furthermore, any failure in the overall BDS, even if it is unrelated to our products, could harm our business. Even after any underlying concerns or problems are resolved, any widespread concerns regarding our technology or any manufacturing defects or performance errors in our products could result in lost revenue, delayed market acceptance, damaged reputation, increased service and warranty costs, and claims against us.

If product liability lawsuits are successfully brought against us, we may face reduced demand for our products and incur significant liabilities.

We face an inherent risk of exposure to product liability claims if our technologies or systems are alleged to have caused harm or do not perform in accordance with specifications, in part because our products are used for sensitive applications. We cannot be certain that we would be able to successfully defend any product liability lawsuit brought against us. Regardless of merit or eventual outcome, product liability claims may result in:

• decreased demand for our products;

• injury to our reputation;

• costs of related litigation; and

• substantial monetary awards to plaintiffs.

Although we carry product liability insurance, if we become the subject of a successful product liability lawsuit, our insurance may not cover all substantial liabilities, which could harm our business.

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If our direct selling efforts for our products fail, our business expansion plans could suffer, and our ability to generate revenue will be diminished.

We have a relatively small sales force compared to our competitors. If our direct sales force is not successful, or new additions to our sales team fail to gain traction among our customers, we may not be able to increase market awareness and sales of our products. If we fail to establish our systems in the marketplace, it could have a negative effect on our ability to sell subsequent systems and hinder the planned expansion of our business.

If our distributor relationships are not successful, our ability to market and sell our products would be harmed and our financial performance will be adversely affected.

We depend on relationships with distributors for the marketing and sales of our products in the Industrial and Clinical markets in various geographic regions, and we have a limited ability to influence their efforts. We expect to continue to rely substantially on our distributor relationships for sales into other markets or geographic regions, which is key to our long-term growth potential. Relying on distributors for our sales and marketing could harm our business for various reasons, including:

• agreements with distributors may terminate prematurely due to disagreements or may result in litigation between the partners;

• we may not be able to renew existing distributor agreements on acceptable terms;

• our distributors may not devote sufficient resources to the sale of products;

• our distributors may be unsuccessful in marketing our products;

• our existing relationships with distributors may preclude us from entering into additional future arrangements with other distributors; and

• we may not be able to negotiate future distributor agreements on acceptable terms.

We may be subject to third-party claims that require additional licenses for our products and we could face costly litigation, which could cause us to pay substantial damages and limit our ability to sell some or all of our products.

Our industry is characterized by a large number of patents, claims of which appear to overlap in many cases. As a result, there is a significant amount of uncertainty regarding the extent of patent protection and infringement. Companies may have pending patent applications, which are typically confidential for the first eighteen months following filing, that cover technologies we incorporate in our products. Accordingly, we may be subjected to substantial damages for past infringement or be required to modify our products or stop selling them if it is ultimately determined that our products infringe a third party’s proprietary rights. Moreover, from time to time, we receive correspondence and other communications from companies that ask us to evaluate the need for a license of patents they hold, and indicating or suggesting that we need a license to their patents in order to offer our products and services or to conduct our business operations. Even if we are successful in defending against claims, we could incur substantial costs in doing so. Any litigation related to claims of patent infringement could consume our resources and lead to significant damages, royalty payments or an injunction on the sale of certain products. Any additional licenses to patented technology could obligate us to pay substantial additional royalties, which could adversely impact our product costs and harm our business.

If we fail to maintain and protect our intellectual property rights, our competitors could use our technology to develop competing products and our business will suffer.

Our competitive success will be affected in part by our continued ability to obtain and maintain patent protection for our inventions, technologies and discoveries, including our intellectual property that includes technologies that we license. Our ability to do so will depend on, among other things, complex legal and factual questions. We have patents related to some of our technology and have licensed some of our technology under patents of others. Our patents and licenses may not successfully preclude others from using our technology. Our pending patent applications may lack priority over applications submitted by third parties or may not result in the issuance of patents. Even if issued, our patents may not be sufficiently broad to provide protection against competitors with similar technologies and may be challenged, invalidated or circumvented.

In addition to patents, we rely on a combination of trade secrets, copyright and trademark laws, nondisclosure agreements, licenses and other contractual provisions and technical measures to maintain and develop our competitive position with respect to intellectual property. Nevertheless, these measures may not be adequate to safeguard the technology underlying our products. For example, employees, consultants and others who participate in the development of our products may breach their agreements with us regarding our intellectual property, and we may not have adequate remedies for the breach. We also may not be able to

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effectively protect our intellectual property rights in some foreign countries, as many countries do not offer the same level of legal protection for intellectual property as the United States. Furthermore, for a variety of reasons, we may decide not to file for patent, copyright or trademark protection outside of the United States. Our trade secrets could become known through other unforeseen means. Notwithstanding our efforts to protect our intellectual property, our competitors may independently develop similar or alternative technologies or products that are equal or superior to our technology. Our competitors may also develop similar products without infringing on any of our intellectual property rights or design around our proprietary technologies. Furthermore, any efforts to enforce our proprietary rights could result in disputes and legal proceedings that could be costly and divert attention from our business.

The United States Government has certain rights to use and disclose some of the intellectual property that we license and could exclusively license it to a third party if we fail to achieve practical application of the intellectual property.

Aspects of the technology licensed by us under agreements with third party licensors may be subject to certain government rights. Government rights in inventions conceived or reduced to practice under a government-funded program may include a non-exclusive, royalty-free worldwide license to practice or have practiced such inventions for any governmental purpose. In addition, the U.S. government has the right to require us or our licensors (as applicable) to grant licenses which would be exclusive under any of such inventions to a third party if they determine that: (1) adequate steps have not been taken to commercialize such inventions in a particular field of use; (2) such action is necessary to meet public health or safety needs; or (3) such action is necessary to meet requirements for public use under federal regulations. Further, the government rights include the right to use and disclose, without limitation, technical data relating to licensed technology that was developed in whole or in part at government expense. At least one of our technology license agreements contains a provision recognizing these government rights.

We may need to initiate lawsuits to protect or enforce our patents, which would be expensive and, if we lose, may cause us to lose some, if not all, of our intellectual property rights, and thereby impair our ability to compete.

We rely on patents to protect a large part of our intellectual property. To protect or enforce our patent rights, we may initiate patent litigation against third parties, such as infringement suits or interference proceedings. These lawsuits could be expensive, take significant time and divert management’s attention from other business concerns. They would also put our patents at risk of being invalidated or interpreted narrowly, and our patent applications at risk of not issuing. We may also provoke these third parties to assert claims against us. Patent law relating to the scope of claims in the technology fields in which we operate is still evolving and, consequently, patent positions in our industry are generally uncertain. We cannot assure you that we would prevail in any of these suits or that the damages or other remedies awarded, if any, would be commercially valuable. During the course of these suits, there may be public announcements of the results of hearings, motions and other interim proceedings or developments in the litigation. Any public announcements related to these suits could cause our stock price to decline.

Our international operations subject us to additional risks and costs.

Our international operations have expanded recently. These operations are subject to a number of difficulties and special costs, including:

• compliance with multiple, conflicting and changing governmental laws and regulations;

• laws and business practices favoring local competitors;

• foreign exchange and currency risks;

• difficulty in collecting accounts receivable or longer payment cycles;

• import and export restrictions and tariffs;

• difficulties staffing and managing foreign operations;

• difficulties and expense in enforcing intellectual property rights;

• business risks, including fluctuations in demand for our products and the cost and effort to conduct international operations and travel abroad to promote international distribution and overall global economic conditions;

• multiple conflicting tax laws and regulations; and

• political and economic instability.

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We intend to expand our international sales and marketing activities, including through our subsidiary in France and our direct sales force in the United Kingdom, and enter into relationships with additional international distribution partners. We may not be able to attract international distribution partners that will be able to market our products effectively.

Our international operations could also increase our exposure to international laws and regulations. If we cannot comply with foreign laws and regulations, which are often complex and subject to variation and unexpected changes, we could incur unexpected costs and potential litigation. For example, the governments of foreign countries might attempt to regulate our products and services or levy sales or other taxes relating to our activities. In addition, foreign countries may impose tariffs, duties, price controls or other restrictions on foreign currencies or trade barriers, any of which could make it more difficult for us to conduct our business.

The nature of some of our products may also subject us to export control regulation by the US Department of State and the Department of Commerce. Violations of these regulations can result in monetary penalties and denial of export privileges.

Our sales to customers outside the United States are subject to government export regulations that require us to obtain licenses to export such products internationally. In particular, we are required to obtain a new license for each purchase order of our biothreat products that are exported outside the United States. Delays or denial of the grant of any required license, or changes to the regulations that make such delays or denials more likely or frequent, could make it difficult to make sales to foreign customers and could adversely affect our revenue. In addition, we could be subject to fines and penalties for violation of these export regulations if we were found in violation. Such violation could result in penalties, including prohibiting us from exporting our products to one or more countries, and could materially and adversely affect our business.

If we fail to retain key members of our staff, our ability to conduct and expand our business would be impaired.

We are highly dependent on the principal members of our management and scientific staff. The loss of services of any of these persons could seriously harm our product development and commercialization efforts. In addition, we require skilled personnel in areas such as microbiology, clinical and sales, marketing and finance. We generally do not enter into employment agreements requiring these employees to continue in our employment for any period of time. Attracting, retaining and training personnel with the requisite skills remains challenging, particularly in the Silicon Valley area of California, where our main office is located. If at any point we are unable to hire, train and retain a sufficient number of qualified employees to match our growth, our ability to conduct and expand our business could be seriously reduced.

If we become subject to claims relating to improper handling, storage or disposal of hazardous materials, we could incur significant cost and time to comply.

Our research and development processes involve the controlled storage, use and disposal of hazardous materials, including biological hazardous materials. We are subject to foreign, federal, state and local regulations governing the use, manufacture, storage, handling and disposal of materials and waste products. We may incur significant costs complying with both existing and future environmental laws and regulations. In particular, we are subject to regulation by the Occupational Safety and Health Administration (“OSHA”) and the Environmental Protection Agency (“EPA”), and to regulation under the Toxic Substances Control Act and the Resource Conservation and Recovery Act in the United States. OSHA or the EPA may adopt regulations that may affect our research and development programs. We are unable to predict whether any agency will adopt any regulations that would have a material adverse effect on our operations.

The risk of accidental contamination or injury from hazardous materials cannot be eliminated completely. In the event of an accident, we could be held liable for any damages that result, and any liability could exceed the limits or fall outside the coverage of our workers’ compensation insurance. We may not be able to maintain insurance on acceptable terms, if at all.

If a catastrophe strikes our manufacturing facilities, we may be unable to manufacture our products for a substantial amount of time and we would experience lost revenue.

Our manufacturing facilities are located in Sunnyvale, California, Bromma, Sweden, and Bothell, Washington. Although we have business interruption insurance, our facilities and some pieces of manufacturing equipment are difficult to replace and could require substantial replacement lead-time. Various types of disasters, including earthquakes, fires, floods and acts of terrorism, may affect our manufacturing facilities. Earthquakes are of particular significance since our primary manufacturing facilities in California are located in an earthquake-prone area. In the event our existing manufacturing facilities or equipment are affected by man-made or natural disasters, we may be unable to manufacture products for sale or meet customer demands or sales projections. If our manufacturing operations were curtailed or ceased, it would seriously harm our business.

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Our short-term investments are subject to risks which may cause losses and affect the liquidity of these investments.

Our short-term investments of $25.0 million, with a fair value of $22.0 million, at June 30, 2009 consisted of auction rate securities. Auction rate securities are securities that are structured with short-term interest rate reset dates of generally less than 90 days, but with contractual maturities that can be well in excess of ten years. Since March 2008, all of our auction rate securities have failed at auction. Our auction rate securities consist of investments that are backed by pools of student loans, which are principally guaranteed by the Federal Family Educational Loan Program (“FFELP”), or insured.

On November 10, 2008, we accepted the offer from UBS to sell the auction rate securities held by us back to UBS at par value beginning June 30, 2010 until July 2, 2012 and the offer to provide “no net cost” loans to us up to 75% of the fair value of the auction rate securities. In accepting the settlement arrangement, we also granted UBS the right to sell our auction rate securities at par at any time up until the expiration date of the rights and released UBS from any claims related to the marketing and sale of auction rate securities, other than claims for consequential damages. We intend to exercise our option and sell the auction rate securities back at par beginning June 30, 2010 through July 2, 2012, depending on market conditions. In the meantime, we entered into a “no net cost” secured line of credit with UBS for $14.7 million, which provides cash liquidity to us until the auction rate securities are resold. Given the substantial disruption in the financial markets and among financial services companies, we cannot assure you that UBS will ultimately have the ability to repurchase our auction rate securities at par, or at any other price, as these rights will be an unsecured contractual obligation of UBS. In addition, changes in fair value of both our auction rate securities and the put option will be recognized in respective period financial results, which could cause fluctuations in the values of these items from period to period.

We might require additional capital to respond to business challenges or acquisitions, and such capital might not be available.

We may need to engage in additional equity or debt financing to respond to business challenges or acquire complementary businesses and technologies. Equity and debt financing, however, might not be available when needed or, if available, might not be available on terms satisfactory to us. In addition, to the extent that additional capital is raised through the sale of equity or convertible debt securities, the issuance of these securities could result in dilution to our shareholders. In addition, these securities may be sold at a discount from the market price of our common stock and may include rights, preferences or privileges senior to those of our common stock. If we are unable to obtain adequate financing or financing on terms satisfactory to us, our ability to continue to support our business growth and to respond to business challenges could be significantly limited.

We rely on relationships with collaborative partners and other third parties for development, supply and marketing of certain products and potential products, and such collaborative partners or other third parties could fail to perform sufficiently.

We believe that our success in penetrating our target markets depends in part on our ability to develop and maintain collaborative relationships with other companies. Relying on collaborative relationships is risky to our future success for these products because, among other things:

• our collaborative partners may not devote sufficient resources to the success of our collaboration;

• our collaborative partners may not obtain regulatory approvals necessary to continue the collaborations in a timely manner;

• our collaborative partners may be acquired by another company and decide to terminate our collaborative partnership or become insolvent;

• our collaborative partners may develop technologies or components competitive with our products;

• components developed by collaborators could fail to meet specifications, possibly causing us to lose potential projects and subjecting us to liability;

• disagreements with collaborators could result in the termination of the relationship or litigation;

• collaborators may not have sufficient capital resources;

• collaborators may pursue tests or other products that will not generate significant volume for us, but may consume significant research and development and manufacturing resources; and

• we may not be able to negotiate future collaborative arrangements, or renewals of existing collaborative agreements, on acceptable terms.

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Because these and other factors may be beyond our control, the development or commercialization of these products may be delayed or otherwise adversely affected.

If we or any of our collaborative partners terminate a collaborative arrangement, we may be required to devote additional resources to product development and commercialization or we may need to cancel some development programs, which could adversely affect our product pipeline and business.

We enter into collaborations with third parties that may not result in the development of commercially viable products or the generation of significant future revenues.

In the ordinary course of our business, we enter into collaborative arrangements to develop new products or to pursue new markets. These collaborations may not result in the development of products that achieve commercial success, and these collaborations could be terminated prior to developing any products. In addition, our collaboration partners may not necessarily purchase the volume of products that we expect. Accordingly, we cannot be assured that any of our collaborations will result in the successful development of a commercially viable product or result in significant additional future revenues in the future.

Compliance with regulations governing public company corporate governance and reporting is complex and expensive.

Many laws and regulations, notably those adopted in connection with the Sarbanes-Oxley Act of 2002 by the SEC and the NASDAQ Global Market, impose obligations on public companies, such as ours, which have increased the scope, complexity, and cost of corporate governance, reporting, and disclosure practices. Our implementation of these reforms and enhanced new disclosures has required and will continue to require substantial management time and oversight and requires us to incur significant additional accounting and legal costs.

ITEM 2. UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS

Not Applicable.

ITEM 3. DEFAULTS UPON SENIOR SECURITIES

Not Applicable.

ITEM 4. SUBMISSION OF MATTERS TO VOTE OF SECURITY HOLDERS

We held our 2009 Annual Meeting of Shareholders (“Annual Meeting”) on April 29, 2009. At the Annual Meeting, shareholders voted on three matters: the election of three Class I directors to serve three-year terms, the approval of the amendment of our 2000 Employee Stock Purchase Plan to increase the number of shares issuable thereunder by 1,500,000 shares, and the ratification of the appointment of Ernst & Young LLP as our independent registered public accounting firm for the fiscal year ending December 31, 2009.

At the Annual Meeting, John L. Bishop, Thomas D. Brown and Dean O. Morton were elected as Class I directors in an uncontested election, by the following votes:

Name	Shares For	Shares Against	Shares Abstaining	Shares Withheld
John L. Bishop	50,939,066	—	—	1,421,414
Thomas D. Brown	51,640,480	—	—	720,000
Dean O. Morton	48,958,636	—	—	3,401,844

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Our Board of Directors is divided into three classes, Class I, II and III directors. Our Class II directors, Thomas L. Gutshall, Cristina H. Kepner, and David H. Persing, and our Class III directors, Robert J. Easton, Mitchell D. Mroz, and Hollings C. Renton, continued their terms following the Annual Meeting.

At the Annual Meeting, the amendment to our 2000 Employee Stock Purchase Plan to increase the number of shares issuable thereunder by 1,500,000 shares was approved by the following vote:

Shares For	Shares Against	Shares Abstaining	Non Votes
33,915,013	4,482,711	48,956	13,913,800

At the Annual Meeting, the appointment of Ernst & Young LLP was ratified by the following vote:

Shares For	Shares Against	Shares Abstaining	Non Votes
52,065,755	229,499	65,206	—

ITEM 5. OTHER INFORMATION

Not Applicable.

ITEM 6. EXHIBITS

(a) Exhibits

Exhibit Number	Exhibit Description	Incorporated by Reference			Filing Date	Filed Herewith
		Form	File No.	Exhibit
10.1	2000 Employee Stock Purchase Plan, as amended	8-K	000-30755	99.1	May 5, 2009
31.1	Certification of Chief Executive Officer pursuant to Rule 13a-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.					X
31.2	Certification of Chief Financial Officer pursuant to Rule 13a-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.					X
32.1*	Certification of Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.*					X
32.2*	Certification of Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.*					X

* This certification accompanying this Report pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 is not deemed filed with the Securities and Exchange Commission and is not to be incorporated by reference into any filing of the Company under the Securities Act of 1933 or the Securities Exchange Act of 1934 (whether made before or after the date of the Report), irrespective of any general incorporation language contained in such filing.

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SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized, in the City of Sunnyvale, State of California on this 4th day of August 2009.

CEPHEID

(Registrant)

/s/    JOHN L. BISHOP

John L. Bishop

Chief Executive Officer and Director

(Principal Executive Officer)

/s/    ANDREW D. MILLER

Andrew D. Miller

Senior Vice President, Chief Financial Officer

(Principal Financial and Accounting Officer)

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Exhibit Index

Exhibit Number	Exhibit Description
10.1	2000 Employee Stock Purchase Plan, as amended (incorporated by reference to Exhibit 99.1 of the Company’s Form 8-K, May 5, 2009).
31.1	Certification of Chief Executive Officer pursuant to Rule 13a-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
31.2	Certification of Chief Financial Officer pursuant to Rule 13a-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
32.1*	Certification of Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.*
32.2*	Certification of Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.*

* This certification accompanying this report pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 is not deemed filed with the Securities and Exchange Commission and is not to be incorporated by reference into any filing of the Company under the Securities Act of 1933 or the Securities Exchange Act of 1934 (whether made before or after the date of the Report), irrespective of any general incorporation language contained in such filing.