Jefferies Healthcare Conference. John Bishop Chairman & CEO June 2, 2014

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Jefferies Healthcare Conference John Bishop Chairman & CEO June 2, 2014 1 Cepheid Cepheid

Worldwide Market Growth by Segment Overall IVD sales are projected to grow at a 5.9% CAGR through 2017. Molecular Diagnostics will remain the highest growth segment. Total = $68.6 B Segment CAGR % Flow Cytometry Immunohematology Histology/Cytology Microbiology Molecular Diagnostics Hem/Coag Clinical Chemistry Immunoassay Point of Care Total = $51.9 B +5.9% CAGR Point of Care (Whole Blood Glucose) 2.3% Point of Care (All other) 8.1% Immunoassays 5.9% Clinical Chemistry 3.4% Hematology/Coagulation 3.0% Molecular Diagnostics 11.9% Microbiology 5.0% Histology/Cytology 9.3% Immunohematology 4.4% Flow Cytometry 6.9% Total Market 5.9% 2 Market Diagnostics 2 International

Worldwide MDx Market Overview Two-thirds of 2012 Molecular Diagnostics market revenue was from diagnostic virology and bacteriology. Discipline 2012 ($ Billion) Percent of Total Total Market: $4.6 Billion Virology $1.7 37% Bacteriology $1.2 26% Genetics/Genomics $0.9 20% Blood Screening $0.8 17% Total Market $4.6 100% 3 Market Diagnostics 3 International

US MDx Laboratory Universe by CLIA Complexity The most significant trend in molecular laboratories during 2012 was the adoption of moderately complex tests by laboratories that had not performed molecular diagnostics in the past. Molecular Laboratories By Testing Menu Total = 2,006 Total = 1,830-3% Highly Complex, with LDT +2% Highly Complex, no LDT Moderately Complex +39% The reduction in labs performing LDTs is attributable to the availability of more FDA-cleared assays such as the Roche TaqMan CMV and the BioFire Respiratory Panel The growth in moderately complex laboratories is the result of the adoption of Meridian and Cepheid assays. Although the BioFire panel is moderately complex it was adopted by labs that already performed one or more molecular assays 4 Market Diagnostics International

Q1 2014: A Solid Start to the Year GeneXpert System Placements +78% Commercial Placements +45% Clinical Revenue +26%, Commercial Clinical +19% Commercial Clinical Xpert Test Revenue +24%* International Commercial Clinical Revenue +47% Continued Menu Execution Xpert HPV, Xpert Norovirus CE-IVD Release in Early April 5 Cepheid * Normalized for Q113 Backorder-Related Revenue

Strategic Drivers GLOBAL MARKET EXPANSION APPLICABLE MARKET EXPANSION MAINTAINING GROWTH LEADERSHIP BROAD MENU EXPANSION 6 Cepheid

Broad Menu Expansion 2 Systems Expansion 1 Test Expansion 3 Remote Connectivity and Data Management 7 Cepheid

Development of Disease Portfolio Other Genetic Disease Oncology Infectious Disease Bacterial Viral Cervical Breast Bladder Prostate Lung 8 Cepheid

Develop The Most Compelling Test Menu Offering. Available Now 2014-2015 2016-17 2018-19 14 MRSA Surveillance SA Nasal Complete C. diff & C. diff/epi vana for VRE MRSA/SA SSTI MRSA/SA Blood Culture EV Flu MTB/RIF CT/NG GBS & GBS Lim Broth Factor II&V 19 Norovirus Carba-R MRSA Surveillance-Next Gen Flu/RSV CW Flu/RSV Trichomonas 33 SA Nasal Complete-Next Gen Pertussis Gastro Panel HSV 1/2 Typing Vaginitis CW Vaginitis CW CT/NG BCR-ABL Ultra Breast CA Stratifier Bladder CA Monitor Bladder CA Symptomatic HPV (Cervical CA) HIV Quant HCV Quant HBV Quant 39 Group A/C Strep Meningitis/Encephalitis GBS Ultra CW GBS Ultra CW Group A/C Strep CW HPV (Cervical CA) Breast CA Signature 16 MRSA Surveillance SA Nasal Complete C. diff/epi vana/vanb for VRE MRSA/SA SSTI MRSA/SA Blood Culture Norovirus (NEW!) EV Flu MTB/RIF CT & CT/NG GBS Factor II&V HPV (Cervical CA) (NEW!) BCR-ABL Monitor 24 Carba-R Trichomonas MRSA Surveillance-Next Gen Flu/RSV Bladder CA Monitor/Sympt BCR-ABL Ultra HIV Quant HIV Qualitative HCV Quant 33 SA Nasal Complete-Next Gen Group A/C Strep Meningitis/Encephalitis Pertussis Gastro Panel HSV 1/2 Typing Vaginitis GBS Ultra HBV Quant Breast CA Stratifier Breast CA Signature 36 Pancreatic CA Monitor EBV / NPC Screen EBV / NPC Monitor = US = International 9 Cepheid Notes: Targeted Test Menu Subject to Revision; CW = CLIA-Waived in Italics Represent Product Improvements and are Excluded from Total Test Counts

Develop The Most Compelling Test Menu Offering. Available Now 2014-2015 2016-17 2018-19 14 MRSA Surveillance SA Nasal Complete C. diff & C. diff/epi vana for VRE MRSA/SA SSTI MRSA/SA Blood Culture EV Flu MTB/RIF CT/NG GBS & GBS Lim Broth Factor II&V 19 33 Norovirus Carba-R Norovirus 19 MRSA Carba-R Surveillance-Next Gen Flu/RSV MRSA Surveillance-Next Gen CW Flu/RSV Trichomonas CW Flu/RSV Trichomonas SA Nasal Complete-Next Gen Pertussis Gastro Panel HSV 1/2 Typing Vaginitis CW Vaginitis CW CT/NG BCR-ABL Ultra Breast CA Stratifier Bladder CA Monitor Bladder CA Symptomatic HPV (Cervical CA) HIV Quant HCV Quant HBV Quant 39 Group A/C Strep Meningitis/Encephalitis GBS Ultra CW GBS Ultra CW Group A/C Strep CW HPV (Cervical CA) Breast CA Signature 16 MRSA Surveillance SA Nasal Complete C. diff/epi vana/vanb for VRE MRSA/SA SSTI MRSA/SA Blood Culture Norovirus (NEW!) EV Flu MTB/RIF CT & CT/NG GBS Factor II&V HPV (Cervical CA) (NEW!) BCR-ABL Monitor 24 24 Carba-R 33 Trichomonas MRSA Carba-R Surveillance-Next Gen Flu/RSV Trichomonas Bladder MRSA CA Surveillance-Next Monitor/Sympt Gen BCR-ABL Flu/RSV Ultra HIV Bladder Quant CA Monitor/Sympt HIV Qualitative BCR-ABL Ultra HCV Quant HIV Quant HIV Qualitative HCV Quant SA Nasal Complete-Next Gen Group A/C Strep Meningitis/Encephalitis Pertussis Gastro Panel HSV 1/2 Typing Vaginitis GBS Ultra HBV Quant Breast CA Stratifier Breast CA Signature 36 Pancreatic CA Monitor EBV / NPC Screen EBV / NPC Monitor = US = International 10 Cepheid Notes: Targeted Test Menu Subject to Revision; CW = CLIA-Waived in Italics Represent Product Improvements and are Excluded from Total Test Counts

GeneXpert System Enables Broad Range of Oncology Opportunities Measure many targets simultaneously ANY other validated RNA expression signature Breast CA Recurrence Signature BCR-ABL Monitor (CML) Sensitively detect translocations in blood Oncology Product Development Using qpcr Decentralized Path using FFPE tissue specimens Breast CA Classifier Prostate CA Recurrence Signature 11 Cepheid Bladder CA Screen At-Risk Bladder CA Symptomatic Bladder CA Monitor Quantitate RNA targets in urine KRAS Pancreatic CA Monitor Quantitate mutations in ctdna Others EGFR, ALK, KRAS Lung CA Monitor

Establishing A Full Global Market Presence Direct Distributed Direct & Emerging Markets Distributed & Emerging Markets 12 Cepheid Emerging Markets

Expanding Scope of Applicable Markets GX-1 Infinity 80 GX-2 Hospitals Infinity 48s GX-4 GX-16 13 Cepheid

Expanding Scope of Applicable Markets Infinity 80 Infinity 48s Independent Labs 14 Cepheid

Industry Leading Throughput and Operating Efficiency 2:1 3:1 4:1 4:1 4:1 Advantage Advantage Advantage Advantage Advantage Infinity-80 Gen Probe Tigris Gen Probe Panther BD Viper Roche Cobas Taqman 96 Abbott m2000 CT/NG Testing Over One 8-Hour shift 15 Cepheid

Menu Application on High Throughput Systems Manufacturer Test Menu On Line Test Capability Cepheid Roche (6800, 8800)* Hologic (Tigris) Qiagen (QiaSymphony RCU) Becton Dickinson (Viper) Abbott (m2000) US:14 EU:17 US: 9 EU:17 US: 6 EU: 6 US: 2 EU: 2 US: 4 EU: 4 US: 8 EU:14 Unlimited 3 4 1 1 1 16 Cepheid * Roche 6600/8800 not yet released.

Expanding Scope of Applicable Markets GX-1 GX-2 Alternate Sites POL s Urgent Care Nursing Homes Retail Outlets Cruise Ships Home GX-4 17 Cepheid

We are a better way. 18 Cepheid Cepheid NASDAQ: CPHD Questions? Contact Investor Relations: investor.relations@cepheid.com or tel. (408) 400 8329