Exhibit 99.01

CEPHEID REPORTS FOURTH QUARTER AND FULL YEAR 2015 RESULTS

Commercial Clinical Grew 19%, or 21% in Constant Currency, Driven by Record Reagent Revenue

and Record GeneXpert System Placements

SUNNYVALE, California, February 2, 2016 – Cepheid (Nasdaq: CPHD) today reported revenue for the fourth quarter of 2015 of $147.0 million, representing growth of 12% from $131.5 million for the fourth quarter of 2014. Net loss was $(9.8) million, or $(0.14) per share, which compares to net loss of $(23.8) million, or $(0.34) per share, in the fourth quarter of 2014.

Excluding stock-based compensation expense, amortization of debt discount and transaction costs, amortization of purchased intangible assets, and a restructuring benefit, non-GAAP net income for the fourth quarter of 2015 was $5.2 million, or $0.07 per share. This compares to non-GAAP net income of $7.8 million, or $0.11 per share, in the fourth quarter of 2014, which excluded stock-based compensation expense, a legal contingency charge, amortization of debt discount and transaction costs, and amortization of purchased intangible assets.

Fiscal 2015 Overview

For the year ended December 31, 2015, Cepheid reported revenue of $538.6 million which compares to revenue of $470.1 million in 2014. Net loss for the year was $(48.5) million, or $(0.67) per share, which compares to net loss of $(50.1) million, or $(0.72) per share, in 2014.

Excluding stock-based compensation expense, amortization of debt discount and transaction costs, amortization of purchased intangible assets, and a restructuring benefit, non-GAAP net income for the full year 2015 was $3.9 million, or $0.05 per share. This compares to a non-GAAP net income of $14.2 million, or $0.19 per share, for the full year 2014, which excluded stock-based compensation expense, a legal contingency charge, amortization of debt discount and transaction costs, and amortization of purchased intangible assets.

“With almost 2,000 GeneXpert Systems placed in 2015, we expect to reach 10,000 GeneXpert System cumulative placements in the first quarter of 2016, highlighting building momentum in customer adoption of the world’s most prevalent molecular diagnostics system,” said John Bishop, Cepheid’s Chairman and Chief Executive Officer. “With up to 23 tests already available on the platform today, we are delivering accuracy, ease-of-use, and flexibility to more customers than ever before. In 2016, we expect to continue to extend our reach into new geographies such as China and Japan, new customer segments including Physician Office Labs and Point-of-Care, and new markets including virology.”

Operational Overview

Business Outlook

For the fiscal year ending December 31, 2016, the Company expects:

Expected non-GAAP net income excludes approximately $43 million related to stock-based compensation expense, approximately $11 million related to the amortization of debt discount and transaction costs, and approximately $5 million related to the amortization of purchased intangible assets. The fully diluted share count for the year is expected to be approximately 73 million in the case of a net loss, and approximately 77 million shares in the case of net income.

The following table reconciles net income (loss) per share to the non-GAAP net income per share range:

Accessing Cepheid’s 2015 Fourth Quarter and Full Year Results Conference Call

The Company will host a management presentation at 2 p.m. Pacific Time on Tuesday, February 2, 2016 to discuss the results. To access the live webcast, please visit Cepheid’s website at http://ir.cepheid.com. A replay of the webcast will be available shortly following the call and will remain available for at least 90 days.

Summary of Management Presentation

In conjunction with today’s press release, the Company is making a summary of the management presentation immediately available at http://ir.cepheid.com.

About Cepheid

Based in Sunnyvale, California, Cepheid (Nasdaq: CPHD) is a leading molecular diagnostics company that is dedicated to improving healthcare by developing, manufacturing, and marketing accurate yet easy-to-use

molecular systems and tests. By automating highly complex and time-consuming manual procedures, the Company’s solutions deliver a better way for institutions of any size to perform sophisticated genetic testing for organisms and genetic-based diseases. Through its strong molecular biology capabilities, the Company is focusing on those applications where accurate, rapid, and actionable test results are needed most, such as managing infectious diseases and cancer. For more information, visit http://www.cepheid.com.

Use of Non-GAAP Measures

The Company has supplemented its reported GAAP financial information with non-GAAP measures that do not include stock-based compensation expense, amortization of debt discount and transaction costs, amortization of purchased intangible assets, a legal contingency charge, and restructuring. The presentation of this additional information is not meant to be considered in isolation or as a substitute for results prepared in accordance with U.S. GAAP. The Company’s management uses the non-GAAP information internally to evaluate its ongoing business, continuing operational performance and cash requirements, and believes these non-GAAP measures are useful to investors as they provide a basis for evaluating the Company’s cash requirements and additional insight into the underlying operating results and the Company’s ongoing performance in the ordinary course of its operations.

These non-GAAP measures may be different from non-GAAP measures used by other companies. In addition, these non-GAAP measures are not based on any comprehensive set of accounting rules or principles. The Company believes that non-GAAP measures have limitations in that they do not reflect all of the amounts associated with its results of operations as determined in accordance with U.S. GAAP and that these measures should only be used to evaluate the Company’s results of operations in conjunction with the corresponding GAAP measures.

As described above, the Company excludes the following items from one or more of its non-GAAP measures when applicable:

Stock-based Compensation Expense. This consists primarily of expenses for stock options and restricted stock under ASC 718 (formerly SFAS 123(R)). The Company excludes stock-based compensation expense from its non-GAAP measures primarily because it is a non-cash expense that the Company does not believe is reflective of ongoing operating results in the period incurred. Further, as the Company applies ASC 718, it believes that it is useful to investors to understand the impact of the application of ASC 718 on its results of operations.

Amortization of Debt Discount and Transaction Costs. The Company incurs amortization of debt discount and transaction costs in connection with the Convertible Senior Notes issued in February 2014. The Company excludes these amounts because these expenses are not reflective of ongoing operating results in the period incurred. These amounts arise from the Company’s issuance of debt and have no direct correlation to the operation of the Company’s business.

Amortization of Purchased Intangible Assets. The Company incurs amortization of purchased intangible assets in connection with acquisitions. The Company excludes these amounts because these expenses are not reflective of ongoing operating results in the period incurred. These amounts arise from the Company’s prior acquisitions and have no direct correlation to the operation of the Company’s business.

Legal Contingency. In the fourth quarter of 2014, the Company recorded a charge for an estimated loss related to ongoing legal proceedings. The Company excluded this item as it believes it is not reflective of ongoing operating results in the period incurred.

Restructuring. The Company excluded a restructuring benefit of $0.1 million in the fourth quarter of 2015 related to a restructuring event recorded in the fourth quarter of 2013. The Company excluded this item as it believes it was non-recurring in nature, and does not have a direct impact on the operation of the Company’s core business.

Forward-Looking Statements

This press release contains forward-looking statements that are not purely historical regarding Cepheid’s or its management’s intentions, beliefs, expectations and strategies for the future, including those relating to projected future growth, future revenues, future net loss/income and profitability and future number of fully-diluted shares, including on a non-GAAP basis, strategic investments, platform features, the breadth and speed of test menu expansion, geographic expansion, customer segment expansion and market expansion. Because such statements deal with future events, they are subject to various risks and uncertainties, and actual results could differ materially from the Company’s current expectations. Factors that could cause actual results to differ materially include risks and uncertainties such as those relating to: the Company’s success in increasing commercial and HBDC sales and the effectiveness of its sales personnel; the relative mix of commercial and HBDC sales, and relative mix of instrument and test sales; manufacturing costs associated with the ramp-up of new products; the performance and market acceptance of new products; the Company’s ability to sell directly to the smaller hospital market and independent reference laboratory market; sufficient customer demand, customer confidence in product availability and available customer budgets for the Company’s customers; the Company’s ability to develop new products, complete clinical trials successfully and obtain regulatory clearances in a timely manner for new products; uncertainties related to the FDA regulatory and international regulatory processes; the level of testing at clinical customer sites, including for Healthcare Associated Infections (HAIs); the Company’s ability to successfully introduce and sell products in clinical markets other than HAIs; long sales cycles and variability in systems placements and reagent pull-through in the Company’s HBDC program; the rate of environmental biothreat testing conducted by the USPS, which will affect the amount of consumable products sold to the USPS; unforeseen supply, development and manufacturing problems; the Company’s ability to manage its inventory levels; the Company’s ability to successfully complete and bring on additional manufacturing lines; the potential need for additional intellectual property licenses for tests and other products and the terms of such licenses; the Company’s reliance on distributors in some regions to market, sell and support its products; the occurrence of unforeseen expenditures, acquisitions or other transactions; costs associated with litigation; the impact of competitive products and pricing; the impact of foreign currency exchange; the Company’s ability to manage geographically-dispersed operations; the Company’s ability to penetrate new geographic markets and manage the operational risks associated with such new markets; and underlying market conditions worldwide. Readers should also refer to the section entitled “Risk Factors” in Cepheid’s Annual Report on Form 10-K, its most recent Quarterly Report on Form 10-Q, and its other reports filed with the Securities and Exchange Commission.

All forward-looking statements and reasons why results might differ included in this release are made as of the date of this press release, based on information currently available to Cepheid, and Cepheid assumes no obligation to update any such forward-looking statement or reasons why results might differ.

FINANCIAL TABLES FOLLOW

CEPHEID

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS

(in thousands, except per share data)

(unaudited)

CEPHEID

CONDENSED CONSOLIDATED BALANCE SHEETS

(in thousands)

(unaudited)

CEPHEID

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

(in thousands)

(unaudited)

CEPHEID

RECONCILIATION OF GAAP TO NON-GAAP MEASURES

(in thousands, except per share data)

(unaudited)