Exhibit 99.01

                                     CEPHEID
                          THIRD QUARTER 2006 CONFERENCE
                         NOVEMBER 2, 2006, 4:30 P.M., ET

Operator                   Good afternoon, ladies and gentlemen, and welcome to
                           the Cepheid third quarter 2006 conference call. At
                           this time, all participants are in a listen-only
                           mode. Following today's presentation, instructions
                           will be given for the question and answer session. If
                           anyone needs operator assistance at any time during
                           the conference, please press the star followed by
                           zero. As a reminder, this conference is being
                           recorded today, Thursday, November 2, 2006.

                           I would now like to turn the conference over to Lasse
                           Glassen with the Financial Relations Board. Please go
                           ahead.

L. Glassen                 Good afternoon. By now you may have seen our press
                           release announcing our results of operations for the
                           third quarter of 2006, which was distributed over the
                           PR Newswire at 4:00 p.m. Eastern time. For your
                           convenience, the press release has also been made
                           available on our website at www.cepheid.com. In
                           addition, a replay of this conference call will be
                           made available later today.

                           During the course of this call, Cepheid will make
                           forward-looking statements. Because such statements
                           deal with future events, actual results might differ
                           materially from those projected in the
                           forward-looking statements. Additional information
                           concerning factors that could cause actual results to
                           differ materially from those in the forward-looking
                           statements can be found in Cepheid's 2005 Annual
                           Report on Form 10-K and in the quarterly reports on
                           Form 10-Q filed with the U.S. Securities and Exchange
                           Commission and in today's press release. Cepheid
                           assumes no obligation to update any such
                           forward-looking statement.

                           With that, it is now my pleasure to introduce
                           Cepheid's Chief Executive Officer, John Bishop. John.

J. Bishop                  Thank you and good afternoon. Joining me on our call
                           this afternoon is John Sluis, our Senior Vice
                           President and Chief Financial Officer.

                           The format for today's call will include an overview
                           of the third quarter and a review of our financial
                           performance for the quarter. This will be
                           subsequently followed with comments on our future
                           outlook for the remainder of 2006 and following these
                           comments we will open the discussion to questions.

                           Reviewing the quarter, our net loss for the third
                           quarter of 2006 was approximately $4.0 million, or
                           $0.07 per share compared to a net loss of
                           approximately $3.3 million, or $0.08 per share for
                           the third quarter of 2005.

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CEPHEID                                                                   PAGE 1



                           As we previously stated, the provisions of SFAS-123R
                           were implemented during the first quarter which
                           resulted in stock compensation expense impacting our
                           operating results for the first time. Accordingly,
                           included in our Q3 net loss for 2006 was $1.6 million
                           of stock compensation expense. Therefore, without
                           stock compensation expense, our non-GAAP Q3 net loss
                           for 2006 was $2.4 million versus a net loss of $3.3
                           million in Q3 2005.

                           Continued strong growth in our clinical product sales
                           coupled with good Q3 performance in industrial sales
                           drove a total product sales increase of 18% for the
                           third quarter over the third quarter of 2005.

                           As we have discussed on prior occasions, installation
                           of Biohazard Detection Systems, or BDS, within United
                           States Post Office, or USPS, processing centers was
                           completed during the fourth quarter of 2005. As
                           expected, no sales of additional GeneXpert modules
                           for the USPS program are planned for 2006. For the
                           three and nine months ended September 30, 2005 sales
                           of GeneXpert modules to the USPS were $3.4 million
                           and $10.0 million, respectively. The program
                           continues to run well with over 3.6 million tests run
                           to date with no false positives. We expect the
                           cartridge utilization rate to be approximately the
                           same in '07 as that realized in 2005.

                           The company achieved a significant milestone during
                           the quarter in the clinical market with the 510(k)
                           clearance from the U.S. Food & Drug Administration or
                           FDA to market the Company's Xpert GBS test for Group
                           B Streptococcus on its GeneXpert system. The
                           Xpert(TM) GBS test was also categorized by the FDA as
                           "moderate complexity" under the Clinical Laboratory
                           Improvement Amendments program. The Xpert GBS test is
                           the first amplified molecular diagnostic test
                           utilizing real time PCR to receive the moderate
                           complexity CLIA categorization. This will allow the
                           assay to be performed by institutions registered for
                           CLIA Moderate Complexity in addition to institutions
                           registered for High Complexity.

                           Delivery of our GX XVI, our new 16 module GeneXpert
                           system, was initiated during the quarter and five
                           systems have been installed in hospital accounts. The
                           company also recently disclosed development of our
                           single module system, the GX I, with an integrated
                           computer, touch screen display and bar code scanner
                           and announced plans to develop a new high volume
                           system.

                           The projected completion of these systems is expected
                           to position Cepheid to develop a single diagnostic
                           product line that can be run in a wide range of
                           laboratory environments, from a doctor's office with
                           a single module system to a high volume central
                           laboratories operating in a hospital setting. While
                           this capability has a number of benefits, a key
                           benefit will be the elimination of the need to
                           correlate test results obtained in a doctor's office
                           or other non-central lab setting to test results
                           generated in the central lab. This historically has
                           been a significant problem in the development of
                           testing in an alternate site setting.

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CEPHEID                                                                   PAGE 2



                           During the quarter, the Company also announced the
                           receipt of a Phase 2 funding from the National
                           Institute of Allergy and Infectious Disease or NIAID
                           for their Small Business Technology Transfer Grant
                           entitled "Sample Processing Cartridges for Rapid PCR
                           TB Detection". Cepheid's academic partner for this
                           program is Dr. David Alland of the University of
                           Medicine and Dentistry of New Jersey. Cepheid and
                           UMDNJ previously announced a program for development
                           of an easy-to-use PCR cartridge that detects the
                           presence of Mycobacterium tuberculosis and also
                           predicts drug resistance in about one hour.

                           This program is being funded by FIND, a Geneva-based
                           non-profit organization partnered with the Bill and
                           Melinda Gates Foundation. The newly awarded NIAID
                           funding will complement these efforts by focusing on
                           development of sample collection devices and on
                           development of proprietary nucleic acid dyes,
                           quenchers, interpretive software and other
                           technologies associated with commercial
                           implementation of a 6-color GeneXpert system.

                           The ultimate goal of both programs is to develop a
                           rapid test with accuracy that is equal to or better
                           than current methods, thus shifting the burden away
                           from culture techniques which require weeks to months
                           to generate the same results.

                           With the advent of ultra drug resistant TB,
                           laboratories are seeking non-culture-based methods
                           for identification because classical methods of
                           identifying this dangerous organism are a hazard to
                           laboratory personnel.

                           Specifically looking at our sales by market for the
                           third quarter, our clinical sales were up by 135% as
                           compared to the third quarter of 2005, reaching $5.8
                           million and represented approximately 26% of our
                           total product sales as compared to 13% of our product
                           sales in the third quarter of 2005.

                           Sales in the Industrial market for the third quarter
                           were up 28% reaching $4.8 million and represented
                           approximately 21% of our total product sales as
                           compared to 19% of total product sales in the third
                           quarter of 2005.

                           Biothreat sales for the third quarter were down by 7%
                           at $12.1 million and represented approximately 53% of
                           our total product sales. This is compared to 68% of
                           total products sales in the third quarter of 2005.
                           The decrease was due to the previously noted
                           completion of the installation of the USPS BDS units.

                           Geographically, our product sales for the third
                           quarter were derived as follows: we had 87% in North
                           America; 10% in Europe; and 3% in Japan and the rest
                           of the world. This is compared to 95% in North
                           America; 3% in Europe; and 2% in Japan and the rest
                           of the world in the prior year quarter.

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CEPHEID                                                                   PAGE 3



                           Our product mix for instruments versus reagents and
                           disposables for the third quarter was 32% for
                           instruments and 68% for reagents as compared to 43%
                           for instruments and 57% for reagents for the prior
                           year quarter.

                           We also announced our first acquisition of technology
                           during the quarter relating to diagnostic markers
                           with the purchase of Actigenics, a small company in
                           Toulouse, France. Actigenics is one of the leaders in
                           the discovery of micro RNAs, a newly identified class
                           of genetic markers that are closely related to gene
                           expression and regulation. Actigenics has developed
                           bioinformatics algorithms that identify proprietary
                           micro RNA candidates with a high degree of
                           confidence, leading to one of the world's largest
                           portfolios of micro RNA diagnostic candidates.
                           Thousands of additional micro RNA candidates have now
                           been identified and are being validated in our
                           discovery pipeline.

                           Recently published studies indicate that micro
                           RNA-based cancer markers may potentially provide the
                           basis for cancer detection, classification,
                           prediction of tumor aggressiveness and determination
                           of treatment susceptibility. In addition, we are
                           pursuing micro RNA-based markers of infection and
                           inflammation.

                           Via this acquisition, Cepheid now possesses both
                           therapeutic and diagnostic rights to approximately
                           150 validated micro RNAs. We currently plan to
                           out-license the therapeutic applications of these
                           micro RNA targets as appropriate. However, we plan on
                           maintaining the opportunity to develop diagnostic
                           tests based on all our validated candidates, whether
                           or not they are linked to such therapeutic
                           applications.

                           Moving to our third quarter 2006 financial
                           performance, John Sluis, our CFO will walk us through
                           our performance highlights.

J. Sluis                   Good afternoon. Total product sales for the third
                           quarter of 2006 increased 18% to approximately $22.6
                           million from $19.2 million for the third quarter of
                           last year and year-to-date sales of approximately
                           $60.8 million represent a 4% increase from the first
                           nine months of last year.

                           As John has mentioned, during the third quarter
                           strong sales growth in the clinical market of 135%
                           combined with a 28% increase in industrial market
                           sales offset the planned decrease in Biothreat
                           product sales due to the cessation in GeneXpert
                           module sales to the United States Postal Service.
                           Adjusting for the GeneXpert module sales for the
                           third quarter and first nine months of 2005 of $3.4
                           million and $10.0 million, respectively, sales of all
                           other products increased 43% during the third quarter
                           and 26% for the first nine months of 2006.

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CEPHEID                                                                   PAGE 4



                           Other revenues decreased 5% to approximately $1.1
                           million for the third quarter of 2006 and decreased
                           6% to approximately $3.0 million for the first 9
                           months of this year as compared to $1.2 million in
                           the third quarter of 2005 and $3.2 million in the
                           first 9 months of 2005. The decrease in other
                           revenues for the quarter was driven by a decrease in
                           grant and government sponsored research revenue.

                           Gross margin, excluding stock compensation expense,
                           on product sales for the quarter of 42% compares to
                           40% for the corresponding prior year quarter. GAAP
                           reported gross margin of 41% for the quarter includes
                           $0.2 million of stock compensation expense.
                           Year-to-date gross margin excluding stock
                           compensation expense was 41% compared to 42% for the
                           first 9 months of 2005. GAAP reported gross margin of
                           40% for the year-to-date includes $0.5 million of
                           stock compensation expense. The increase in gross
                           margin for the third quarter was due primarily to a
                           more favorable product mix compared to the third
                           quarter of 2005. The decrease in gross margin for the
                           nine months of 2006 was due to a slightly unfavorable
                           product mix over the full course of the first nine
                           months of this year.

                           Research and development expenses for the quarter
                           were $5.6 million, which is $0.8 million or 17%
                           higher, of which $0.6 million is attributed to stock
                           compensation expense. During the third quarter,
                           Actigenics acquisition related expenses of $0.2
                           million were recorded in the quarter with $45,000 of
                           amortization expense recorded as R&D expense and
                           $139,000 shown separately as expensing of in-process
                           technology. R&D expenses for the first nine months
                           were $17.2 million which is $3.4 million or 25%
                           higher than the same period last year of which $1.9
                           million is stock option expense. The remainder of the
                           increase for the first nine months is due to the
                           increase in clinical trial expense for the GeneXpert
                           GBS and Enterovirus assay 510(k) submissions to the
                           FDA.

                           SG&A expenses of $6.1 million were $1.6 million or
                           36% greater than the third quarter of 2005. Out of
                           this $1.6 million increase, approximately $0.8
                           million was attributed to stock compensation expense.
                           Year-to-date SG&A expenses of $19.2 million were $5.1
                           million or 36% greater for the first nine months of
                           2005, of which $2.7 million was due to stock
                           compensation. The remaining increases were primarily
                           due to an expansion of our direct salesforce,
                           increased marketing and product support personnel and
                           promotional costs to support the clinical market.
                           Also included were increases of course in G&A
                           expenses.

                           Collaboration profit sharing expense of $3.8 million
                           and $11.5 million for the quarter and year-to-date
                           compared to $2.9 million and $10.1 million for the
                           same period last year, and represents the sharing of
                           gross margin on biothreat cartridge sales with
                           Applied Biosystems in accordance with our
                           collaboration agreement.

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CEPHEID                                                                   PAGE 5



                           As John has mentioned, Net loss excluding stock
                           compensation expense for the third quarter of 2006
                           was approximately $2.4 million compared to a net loss
                           of approximately $3.3 million for the third quarter
                           of 2005. GAAP reported net loss of $4.0 million
                           includes $1.6 million of stock compensation expense
                           and in total results in a net loss of $0.07 per
                           share. Year-to-date net loss excluding stock
                           compensation expense of $12.5 million compares to a
                           net loss of $10.4 million or $0.24 per share for the
                           first 9 months of 2005. GAAP reported net loss was
                           $17.7 million or $0.34 per share. Included in the net
                           loss for the quarter and nine months of 2006 is $0.2
                           million of Actigenics related acquisition expense.

                           Turning to the balance sheet, total unrestricted cash
                           and marketable securities as of September 30, 2006
                           was $98.4 million.

                           And now back to John.

J. Bishop                  Moving to our current outlook for 2006 and beyond,
                           subsequent to the close of the quarter, the Company
                           announced the European release of the Xpert MRSA or
                           Methicillin-resistant Staphylococcus aureus test for
                           clinical diagnostic use on the GeneXpert System. The
                           MRSA test was released as a CE IVD Mark product under
                           the European Directive on In Vitro Diagnostic Medical
                           Devices. The Xpert MRSA test is designed to rapidly
                           detect MRSA in patients for surveillance programs to
                           aid in the reduction of hospital acquired infections
                           or HAI.

                           We continue to expect to complete U.S. clinical
                           trials for the Xpert MRSA test by the end of the year
                           and to submit a 510(k) application to the FDA during
                           the first quarter 2007.

                           We also continue to expect to receive word on our
                           regulatory submission for enterovirus meningitis on
                           the GeneXpert System by the end of the year.

                           The GeneXpert system continues to be well received
                           and installation of 52 clinical systems representing
                           234 operating modules have been completed in the U.S.
                           and Europe.

                           We continue to expect our 2006 product sales to be in
                           the range of $83.0 million to $86.0 million based on
                           anticipated sales from existing and new products and
                           sales expected from the USPS program. We expect our
                           2006 net loss to be in the range of $12.0 to $14.0
                           million or $0.23 to $0.27 per share based on expected
                           weighted average shares outstanding of 52.3 million
                           for the year ended December 31, 2006. This is
                           inclusive of additional interest income to be
                           generated from the proceeds of our follow-on
                           offering, but does not include any expenses
                           associated with the Actigenics acquisition.

                           I would now like to open the call for your questions.
                           Operator, do we have any questions at this time?

Operator                   Thank you. Ladies and gentlemen, at this time we'll
                           begin the question and answer session. If you have a
                           question, please press the star key followed by one
                           on your pushbutton phone. If you would like to
                           decline from the polling process, press the star
                           followed by two. You will hear a three-toned prompt
                           acknowledging your selection. Your questions will be
                           polled in the order they are received. If you are
                           using speaker equipment, you will need to lift the
                           handset before pressing the numbers.

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CEPHEID                                                                   PAGE 6



Operator                   Our first question comes from Quintin Lai with Robert
                           W. Baird. Please go ahead.

Q. Lai                     Good afternoon. With respect to the installations in
                           this quarter and then what you just gave with update
                           on the 52 installations in the U.S. and Europe, so
                           are those addition installations year-to-date, I
                           guess inclusive of what's going on in the fourth
                           quarter?

J. Bishop                  Those are inclusive of what's going on in the third
                           quarter, Quintin, as we really didn't get going.
                           We've been moving somewhat in Europe with the
                           GeneXpert program. We nearly didn't get going in the
                           U.S., as you may be aware, until the July timeframe
                           when the GBS was cleared in the U.S. market so I
                           would look at those installations as primarily
                           ramping from the summer timeframe.

Q. Lai                     Okay. And then for the field installations that you
                           do have that are now running Group B Strep, what are
                           the early returns on how the instrument is preforming
                           and have they been catching Group B Strep?

J. Bishop                  Well we're early right now because actually as we
                           look at the institutions on Group B Strep
                           specifically we have a mixture of accounts that are
                           running. I mean if you look at Europe you're mixing
                           in EV, BCR-able as well as the Group B Strep. Right
                           now in the U.S. specifically on the Group B Strep
                           situation in the U.S. market, there's about 16
                           accounts who've elected to initiate testing with
                           Group B Strep and as you're aware, they go through a
                           validation process to integrate the test into their
                           laboratory settings so they're currently in that
                           validation start up mode.

                           Now in addition behind that we've got about 54
                           accounts that are currently past the qualification
                           stage and they're somewhere in the sales process at
                           this point.

Q. Lai                     And of those ones that are in the process of looking
                           at adopting or putting it in, are they taking
                           advantage of the moderate complexity label that
                           GeneXpert has or are they mainly high complexity labs
                           that are looking at this right now?

J. Bishop                  The initial ones are mainly high complexity labs. We
                           haven't had some of the moderate complexity labs
                           picking up as yet. I would put those in likely a
                           second tier setting.

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CEPHEID                                                                   PAGE 7



Q. Lai                     Okay. And my final question is you did mention that
                           the guidance excludes the cost of Actigenics. Can you
                           help us out with what to expect on the cost of
                           Actigenics in the fourth quarter?

J. Sluis                   Well from a standpoint of amortization of intangibles
                           it'll be somewhat minimal, in the neighborhood of 40
                           or 50. We really are focusing on the third quarter
                           there as it extends to the full year in which we were
                           slightly under $0.2 million.

Q. Lai                     Okay. Thank you.

Operator                   Our next question comes from Derik de Bruin with UBS
                           Please go ahead.

D. de Bruin                Hi. I was wondering if you could give us an update on
                           the fiscal '07 Post Office contract. What have you
                           heard on that and give us some color?

J. Bishop                  Certainly. We're actually anticipating right now,
                           we've received an interim bridging purchase order
                           that we've been shipping against because we completed
                           the other purchase order for this year in September
                           so we're currently shipping against the bridging
                           purchase order and we expect to have the full blown
                           purchase order covering the remainder of '06-'07
                           period in virtually any day at this point. Our
                           current expectation is that the cartridge volume in
                           the '07 timeframe will be essentially the same as the
                           cartridge volume as seen in the '06 timeframe.

D. de Bruin                Okay, that's very helpful. Now do you have any idea
                           if they're going to be using ... do you have any
                           indication right now if there's a potential of them
                           using the 3 agent test?

J. Bishop                  I think likely, Derik, that they're going to continue
                           to be using the anthrax only cartridge, not the 3
                           agent cartridge going forward. They right now haven't
                           shown what I would say would be a high level of
                           interest in expanding much beyond the anthrax
                           determination.

D. de Bruin                Okay. You know you had some nice gross margin
                           improvement, sequential gross margin improvement. I
                           guess how do you see the gross margins ramping from
                           here on out?

J. Sluis                   Basically what we're looking at of course is an
                           improvement in the product mix for our clinical
                           products, basically ones that we have developed and
                           are self-manufactured. Those will carry higher
                           margins than our other products.

                           Secondly, as overall volumes increase, that affects
                           the cost of all of our products. It'll also help to
                           improve our margins. So looking forward we see
                           ourselves basically improving our margins with the
                           increase in clinical sales as the percentage of our
                           total product mix and the overall increase in sales
                           in total.

D. de Bruin                Okay. And when you look at the level of SG&A and R&D
                           spending, do you think you need to ramp significantly
                           to meet your current expectations in terms of
                           clinical trials or salesforce in order to get the
                           GeneXpert launched?

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CEPHEID                                                                   PAGE 8



J. Sluis                   The GeneXpert ... first of all on the R&D side
                           probably the most significant R&D expense impact will
                           be clinical trial expense and of course we will see
                           that as we go into clinicals with MRSA that will last
                           until that process is complete.

                           In terms of SG&A expenses, probably the most
                           significant expenses there of course will be in
                           promoting our new clinical products and we should see
                           increases in commission expenses and promotional
                           expenses accordingly.

D. de Bruin                Okay. And finally could you update us on the combo
                           test?

J. Bishop                  The combo test right now we're putting primary focus
                           on getting the MRSA test through the clinicals and
                           into the FDA. Work has been initiated on the combo
                           test so that'll get more fully up to speed once we
                           get the single test into the FDA in the first
                           quarter.

                           I might as well take advantage as the question there,
                           Derik, and comment on we had some calls today and
                           some questions on the new CDC guidelines with regard
                           to drug resistant detection and prevention in the
                           hospital setting.

                           The new guidelines that came out on October 19th
                           actually are one of about 5 initiatives, various
                           government initiatives involved in this area. We have
                           one initiative which is having to do with mandatory
                           reporting of hospital acquired infections. Right now
                           there's about 15 states with actual mandatory
                           reporting requirements. There's 5 with study bills
                           and about another 15 states with legislative
                           activities. So a lot of action in this area. As these
                           things develop we believe that it could have
                           potential strong impact on the development of the
                           market.

                           There's some things I'll talk about in a second with
                           regard to the CDC guidelines, but then in addition,
                           there's the Centers for Medicare/Medicaid Services
                           initiative which actually could be implemented in
                           October 2008 and this initiative would call for
                           reductions in Medicare DRG acuity assignments and
                           payments for hospital acquired infections that
                           occurred during the patient's stay. So certainly that
                           could have some substantial impact on the speed of
                           market adoption rates in this area.

                           The other item that I would call out to you
                           specifically is on Page 10 of the CDC guidelines
                           where they're calling for a 4-phased program to help
                           control and prevent the infections and those 4 phases
                           are infection prevention, #1. Number 2, accurate and
                           prompt diagnosis and treatment. Number 3, prudent use
                           of antimicrobials, and 4, prevention and
                           transmission. So as a key thing in there with regard
                           to the accurate and prompt diagnosis because as one
                           reads through the guidelines, one of the primary
                           immediate near term interest and focus is in the ICU
                           units and there that means that you need to have
                           immediately available, 24/7 capability to be able to
                           run these tests. And that means that you really need
                           to be moving away from batch type of testing and be
                           able to do testing which really fits very nicely with
                           the GeneXpert System on being able to do testing as
                           the requirement arises.

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CEPHEID                                                                   PAGE 9



                           So we're looking at an interesting opportunity and
                           that's why right now we're really focused on getting
                           the initial MRSA product aggressively on the market
                           in the U.S. as we already have in Europe.

D. de Bruin                Great. Thank you very much. I'll get back in the
                           queue.

Operator                   Dan Owezarski with Soliel-Belmont Harbor Capital.
                           Please go ahead.

D. Owezarski               Thanks. Hi, John, hi, John. Can give us an idea in
                           the industrial area who was buying this quarter or
                           really for what kind of usage and should we see it
                           cool off in the next quarter or is it kind of back to
                           normal now?

J. Bishop                  Let me answer your question, the last part of your
                           question first. Frankly we're not unusual in that
                           regard. I mean if you go talk to any number of the
                           life sciences companies where that's much more the
                           full focus of their business, there's a lot of
                           concern these days about overall government funding
                           going into the research areas, a lot of concern about
                           reductions in NIH funding.

                           So I believe that what you're likely going to see in
                           the industrial marketplace not only for ourselves,
                           but for others would be what I call a choppy effect.

                           I think you're going to see some quarters that may be
                           down and others that may be up depending upon the ebb
                           and flow of government funding and specific research
                           programs that end up getting funded during a quarter
                           because also with this we've seen shifting in funding
                           that takes place.

                           So on a similar vein in our last third quarter we've
                           seen they're similar as we have in the past. The
                           sales went into a number of research based programs
                           as well as government surveillance programs.

D. Owezarski               Can you give us any insight as to any specific areas
                           that there was purchasing going on in that industrial
                           area?

J. Bishop                  Not that I would comment on for you right now because
                           it was actually a pretty broad application. We had
                           everything ranging from water testing environmental
                           areas to basic research and looking at other types of
                           environmental tests.

D. Owezarski               Okay. And then to switch to MRSA and the FDA review,
                           do you expect to get any benefit? Could that be
                           shorter now that you have Group B Strep through the
                           pipeline and under your belt? Do you get any benefit
                           from this being kind of your second, third submission
                           to the FDA as far as shortening these timetables for
                           review?

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CEPHEID                                                                  PAGE 10



J. Bishop                  The short answer to that would be yes that would be
                           the expectation. We took longer, our actual time post
                           the date of log-in from the FDA on the Group B Strep
                           was 146 days there, but that was a first in class and
                           they had to establish a whole new classification
                           which has now been done for amplified moderate
                           complexity molecular tests.

                           So I would expect that we should get the benefit of
                           the classification that's already been established as
                           we go forward with the MRSA. Now I should also
                           comment looking at the EV, I mean we've now been
                           there 199 days since the initial log-in date to the
                           FDA, but this is another example of a first in class
                           type of determination in the viral area.

D. Owezarski               Okay. And then to move to the GX-1, do you have a
                           timetable as to development, product launch or even
                           just rough guideline there?

J. Bishop                  Rough guideline on that one would be that we would
                           expect to be delivering the product around the fourth
                           quarter of next year '07.

D. Owezarski               And then for John Sluis just one last one. On SG&A it
                           looked like it was down pretty well on a sequential
                           basis dramatically. Was there a one time charge?
                           Could you refresh our memories in the second quarter
                           of why is the difference sequentially down here?

J. Sluis                   For SG&A I'm taking a look at that. I think from the
                           standpoint of we probably were looking at some
                           increased expenses in two areas. First would be legal
                           expenses as we pursue resolution of a couple of items
                           and secondly in the financial area, we did extensive
                           work in accounting for purposes of documentation for
                           S-Ox 404 requirements and both of those combined can
                           add significant cost. And also selling was a strong
                           push in the second quarter and as a result a little
                           bit of a bulge there, yes.

D. Owezarski               Okay. And then how should we think about it just
                           going forward the next couple quarters? More like
                           this quarter?

J. Sluis                   That's what we anticipate at this point, correct.

D. Owezarski               Great. Thank you.

Operator                   Our next question comes from Jason Weiss with Robert
                           W. Baird. Please go ahead.

J. Weiss                   Good afternoon. Earlier today BD was talking about a
                           pilot program they're doing with the VA hospitals
                           where they're working right now with 18, but
                           potentially 170 or so by the end of '07 for
                           eradicating MRSA. Could you help us, let us know how
                           to think about how you might be participating in that
                           and what it could mean for you?

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CEPHEID                                                                  PAGE 11



J. Bishop                  Certainly, Jason. First off one needs to understand
                           the overall market dynamics. On the program that BD
                           was evidently talking about of course right now that
                           would be specific to them on utilizing the
                           SmartCycler based batch approach, going into
                           screening on that program. The problem once they're
                           running there then as you look at need for immediate
                           diagnosis ,that means you need to be running 24/7.

                           Now to walk you through how we see the market
                           developing there. Primarily if one were to focus just
                           on ICU patients, which is a key focus for the CDC,
                           that's about 5.3 million test opportunities annually.
                           As we would see the market potential there around
                           $180 million. Then if you looked at all high risk
                           patients, which would include those coming in for
                           surgical procedures, that's about 10.5 million or
                           $357 million. Now if you moved, and there's right now
                           probably only about 2 or 3 accounts that are doing
                           testing screening of all patients coming into the
                           hospital, one of which is Evanston Northwestern which
                           is actually using the BD product. A second one is
                           Mayo Clinic has actually decided to go with culturing
                           techniques. And an all admissions program would bring
                           the market U.S. only to about just short of $1.2
                           billion opportunity.

                           Now as we look at Europe, the actual number of
                           admissions into institutions in Europe are actually a
                           little greater than in the U.S. market. So the
                           European market could potentially be in this case
                           larger than the U.S. market opportunity and that
                           would put the market just between the U.S. and Europe
                           at something a little over a $2 billion market
                           opportunity.

                           So our view there is we are positioned to very
                           effectively compete and take part in what is a
                           rapidly developing market.

                           The key thing there with the GeneXpert and that's one
                           of the beauties of it is that uniquely as one moves
                           to implement testing within the hospital setting,
                           there's a need to potentially run centralized lab
                           testing. There's a need to potentially disseminate
                           and get a test capability out and get it right in a
                           stat lab or an ICU type of a setting situation. And
                           that's perfect for the GeneXpert because it gives the
                           institution the ability to take the same exact test,
                           use it in all of those settings, not have any
                           problems in correlating the overall results to get
                           that benefit.

                           So we're looking right now at ... the GX-16 is well
                           positioned already to meet those market needs because
                           if you look at the admission rates for high volume
                           hospitals, I mean some of the largest hospitals in
                           the country you're admitting about 165 patients a
                           day. In that setting we're looking at the 16 being
                           able to easily handle that volume and then
                           subsequently we'll be coming with the GX-HV.

                           So we view all this and frankly any time you're
                           developing a new market opportunity, two companies
                           moving rapidly to help develop the market are going
                           to be more effective versus just one.

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CEPHEID                                                                  PAGE 12



J. Weiss                   Great. And then just as a follow on to that actually
                           kind of what you're going at at the end of your last
                           comment. Do you see that the education in the
                           marketplace among hospitals with the new CDC
                           guidelines may give you some momentum coming into the
                           beginning of 2007 when the MRSA approval is expected?

J. Bishop                  I would say that the answer to that is yes and don't
                           forget I mentioned that the new CDC guidelines are
                           only the latest of what are like 5 different
                           guidelines. So right now you've got the legislative
                           activity that's underway that we're already talking
                           about. You've got the CDC we just talked about now.

                           Then you also have the SHEA guidelines which is the
                           Society for Healthcare Epidemiology of America. They
                           have some similar guidelines somewhat to the CDC. And
                           then you have the APIC initiative on MRSA. And then
                           finally, the CMS initiative on the Medicare/Medicaid
                           reimbursement which would then be not fully covered
                           for patients contracting the hospital acquired
                           infection while they're there.

                           So I think all of these initiatives are helping to
                           much more rapidly educate the market as to the need
                           and the benefits of initiating testing.

                           I think it was also interesting that when you look at
                           again the CDC guidelines also on Page 11 where
                           they're giving the actual results, where they call
                           out the results in The Netherlands, Belgium and
                           Denmark, where in those counties they actually don't
                           even admit patients into the general population. They
                           put them in quarantine until they get the results by
                           culture and then put them into the general
                           population. As a result, you get a very low incidence
                           of MRSA in those countries.

                           This is where right now we see the GeneXpert as
                           having a good opportunity over there because that's
                           obviously an immediate market opportunity we're going
                           to be focused on. They're already doing that,
                           incurring the cost of waiting on cultures and we can
                           get those results now substantially faster with the
                           GeneXpert program.

                           Also thought it was interesting that they've called
                           out in a study that was done here in the U.S. on VRE
                           a reduction in prevalence in participating
                           institutions from 2.2% in 1997 to 0.5% in 1999 which
                           clearly shows the efficacy and the benefit of these
                           programs and that's going to translate into
                           substantial savings for the hospital institutions.

J. Weiss                   Great. Well thank you for taking my questions and
                           congratulations on a great quarter.

J. Bishop                  Thank you.

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CEPHEID                                                                  PAGE 13



Operator                   Our next question Zarak Khurshid with Caris and
                           Company. Please go ahead.

Z. Khurshid                Hi, John, hi, John. Congratulations on a nice
                           quarter.

Management                 Thank you.

Z. Khurshid                You spoke a little bit about the EV review, currently
                           199 days. Can you maybe give us some more color on
                           why you think it's taking a little longer than GBS?

J. Bishop                  Yes. As I mentioned there, this is another first in
                           class vis-a-vis a viral detection. A number of people
                           have actually looked at EV historically and this is
                           going to be one of the first ones to go through the
                           FDA via the regulatory pathway for EV. Most of the
                           testing that's done in fact out there today is all
                           home brew so given that it's going to be one of the
                           first and as we've seen with the GBS, it's taking a
                           little longer.

Z. Khurshid                Okay. And then with respect to the GeneXpert clinical
                           placements, to what extent do you think customers are
                           waiting for the EV test and the expanded menu before
                           they invest in the instrument?

J. Bishop                  I think that we have actually a number of them right
                           now I think from what we're seeing, the EV while it's
                           a smaller overall market opportunity, something in
                           the $40-$50 million range, it's extremely medically
                           valuable. So we have a number of institutions that
                           are actually very interested in getting the GeneXpert
                           as soon as that EV test is available. And then I
                           think where you're going, and we would agree, would
                           be the obvious. Once you have the system already
                           placed then it's going to be a lot easier to pull
                           through other tests. So if you have an institution
                           who is interested in GBS, but not enough to go ahead
                           and make the acquisition, they make it for the EV
                           then it may pull through the GBS testing after the
                           fact.

Z. Khurshid                Right. And then with regards to it sounds like MSRA
                           is on track. Any thoughts to the next test in line
                           beyond?

J. Bishop                  Well yeah, actually when we come in February with our
                           '07 guidance expectation, I'd like to give you a
                           better view of that. We're right now in the midst of
                           our '07 operating plan, but I mean we've already
                           indicated we're going to be going back immediately
                           and working on the multiplex MRSA.

                           This would be the one that would be the combo
                           MRSA/MSSA, along with the MEC determination. The
                           other thing that we want to do, and those will likely
                           be in the nasal area.

                           The other thing that there's a big demand upcoming
                           for wounds, both in the hospital,but frankly more
                           specifically with community acquired. There's a real
                           need, rapidly developing need for being able to test
                           almost in an emergency room setting and potentially
                           moving even to a doc's office scenario where we're
                           seeing development of fourth generation antibiotics
                           and these antibiotics are only going to be utilized
                           with a direct correlation to a test.

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CEPHEID                                                                  PAGE 14



                           So I think what we're going to be seeing here is a
                           true pharmacogenomic utility as well going forward so
                           that's squarely in our sights at this point in time.

                           Other things that we're going to be working on will
                           be following up in the hospital acquired infection
                           area, certainly looking at VRE and C. difficile.

Z. Khurshid                Great. Then lastly, John, I missed the breakout of
                           the stock options expense. Could you just quickly
                           break that out?

J. Sluis                   Yeah. For the quarter it was roughly 1.6 million and
                           for the year-to-date it's 5.2.

Z. Khurshid                And then within the operating lines?

J. Sluis                   Okay. Gross margin we had approximately $0.2 million
                           for stock option expense for the quarter and for the
                           year-to-date it's $0.5. In R&D we have $0.6 million
                           of R&D expense and for the year-to-date we're looking
                           at $1.9. Total SG&A is $6.1. We have $0.8 million of
                           stock compensation expense for the quarter and I'm
                           looking here ...

Z. Khurshid                That's fine. Thanks for taking the call, guys.

J. Sluis                   And $2.7 for the 9 months by the way.

Operator                   Management, at this time there are no further
                           questions. I would like to turn the conference back
                           over to you for any additional comments.

J. Bishop                  Thank you. We certainly appreciate your participation
                           in the call today. Lasse, are you going to cover the
                           call-in logistics for replay?

L. Glassen                 Yes, sir. We would like to thank you. As a reminder,
                           this call will be made available for replay after
                           7:30 p.m. Eastern time by calling 1-800-405-2236 for
                           domestic callers or 303-590-3000 for international
                           callers. The replay pass code is 11073987. This will
                           be available until November 9, 2006. The call will
                           also be available on our website at www.cepheid.com
                           through November 2, 2007.

                           Thank you very much for joining us today.

Operator                   Ladies and gentlemen, this concludes today's
                           teleconference. Thank you for participating. You may
                           now disconnect.

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CEPHEID                                                                  PAGE 15