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Executives

Eric Hoffman - Director Investor Relations

James C. Mullen - President, Chief Executive Officer, Director

Paul J. Clancy - Chief Financial Officer, Executive Vice President - Finance

Robert A. Hamm - Chief Operating Officer

Alfred Sandrock, MD, PhD - SVP Neurology R&D

Analysts

Eric Schmidt - Cowen And Company

Joel Sendek - Lazard Capital Markets

May-Kin Ho - Goldman Sachs

Geoff Meecham - J.P. Morgan

Geoffrey Porges - Sanford Bernstein

Mark Schoenebaum - Deutsche Bank Securities

Josh Schimmer - Leerink Swann

Yaron Werber - Citi

Jason Zhang - BMO Capital Market

Jim Birchenough - Barclays Capital

Christopher Raymond - Robert W. Baird & Co., Inc.

Steven Harr - Morgan Stanley

Eun Yang - Jefferies & Co.

Michael Aberman - Credit Suisse

Maged Shenouda - UBS

Rachel McMahon - Banc of America Securities

Biogen Idec Inc. (BIIB) Q3 2009 Earnings Call October 20, 2009 8:30 AM ET

Operator

Good morning ladies and gentlemen my name is Nicollet and I will be your conference operator today. At this time I would like to welcome everyone to the Biogen Idec Inc. Q3 2009 Earnings Conference Call. (Operator Instructions). I would now like to turn the call over to Eric Hoffman. Please go ahead sir.

Eric Hoffman

Thank you and welcome to Biogen Idec’s Third Quarter 2009 Earnings Conference Call. Before we begin, I’d encourage everyone to go to Investor Relations section of biogen.com to find the press release and related financial tables including a reconciliation of the non-GAAP financial measures that we’ll discussed today. We have also posted slides on our website that outline the topics discussed on today’s call.

As usual, we’ll start with the Safe Harbor statement. Comments made in this conference call include forward-looking statements about our expected future results including our 2009 financial guidance, our longer-term operational and financial goals; the sales potential of TYSABRI and other products; the potential markets for our products, pipeline advancements, and regulatory actions.

These statements are subject to risks and uncertainties which could cause actual results to differ materially from expectations. You should carefully review the risks and uncertainties that are described in our earnings release, and in the risk factors section of our most recent annual and quarterly reports filed with the SEC. We do not undertake any obligation to publicly update any forward-looking statements.

Today on the call I’m joined by Jim Mullen, CEO of Biogen Idec; Dr. Al Sandrock, Senior Vice President and Head of our Neurology R&D organization; Bob Hamm our Chief Operating Officer; and Paul Clancy, CFO and Executive Vice President of Finance.

With that, I’ll turn the call over to Jim Mullen.

Jim Mullen

Thanks Eric, good morning everyone. I am pleased to be able to report another solid quarter continuing on our Q2 performance. Not only was our financial performance strong, but we also made progress on our pipeline. Total revenue grew to more than $1 billion in non-GAAP EPS for the third quarter 2009, it was up 14% over last year to $1.12. Importantly, we remain on track to achieve our full year operating plans.

AVONEX revenues were $580 million supported by the long-term safety and efficacy profile. In the US AVONEX continued to see market share decline and we are working towards improvements here as our CEO Bob Hamm will detail in his comments, and we think this performance can be turned around.

In addition AVONEX performance was impacted by growth in our Access Program that provides free drugs to patients who cannot afford the therapy. As we have discussed before this correlates closely with unemployment trends.

Internationally AVONEX has picked up market share and continues to grow in volume. This is important because the international MS market is both larger and growing more rapidly than the US market. We were pleased to have our method of use patent issued in the US covering AVONEX through 2026 and Bob will discuss the implications.

TYSABRI patient growth continued through the summer nearly 3,000 net new patients were added in Q3 for a total of approximately 46,200 patients currently on therapy or a 30% growth year-over-year. We achieved TYSABRI global end market net sales in the quarter of more than $282 million up 19% year-over-year resulting from the continued success of our marketing and sales efforts focused on TYSABRI’s compelling efficacy. We booked $207 million of this net of hedge on our P&L.

Internationally we saw some expected seasonality over the summer as net new patients added dipped in August and then recovered in September. We continue to look for and evaluate methods and approaches to further identifying risk factors for PML which Al Sandrock the lead to our Neurology R&D organization will speak to later.

Revenue from the RITUXAN unconsolidated joint business was $284 million on net US sales of $670. Bob Hamm will also take you through an update on our commercial franchise.

Our pipeline progressed nicely during the quarter. Strategically our pipeline is focused on first in class or best in class specialty products in diseases with high-unmet need and global applications. I will provide a couple of examples of recent positive developments and upcoming milestones.

Yesterday we and our partner Biovitrum announced the positive read out on our Phase I/II study of our long acting Factor IX for hemophilia B and planned to advance the program into registrational trial in 2010.

Last week our partner Acorda had successful FDA Advisory Committee on Fampridine-SR in MS and we plan to file with the MEA in early 2010.

We completed enrollment in the third quarter for CONFIRM the second of the two Phase III trials of our oral BG-12 in MS and we are especially pleased with this accomplishment given the size and complexity of the BG-12 Phase III program. Final read outs are expected by year-end that will include a Phase II study of Ocrelizumab for MS.

Al Sandrock will give you updates on a number of pipeline programs including these and others.

We are reiterating our 2009 non-GAAP earnings per share to be above $3.85 and we continue to expect cash flow from operations to exceed earnings. Our CFO Paul Clancy will give you additional financial details.

Also, this morning we are announcing a share repurchase related to our approximately $3 billion cash balance our board has authorized a share repurchase of up to $1 billion in order to return excess cash to shareholders. We expect to implement this buy back over the coming months to reduce the share count over time. This program does not impact our ability to execute against strategic external growth opportunities, but represents the strength we see in the ability of our core products to generate significant cash flow for the Company. Paul will discuss this in more detail during his comments.

In conclusion, the third quarter was a successful one and we are reiterating full year 2009 guidance. Our main focus was maintaining TYSABRI patient growth and we accomplished that goal. We have strong franchises, cash flow on the balance sheet, and ended the quarter with approximately $3 billion in cash and marketable securities and we continue to focus on products pipeline performance as drivers of long-term shareholder value creation.

I will now hand the call to Dr. Al Sandrock, SVP Neurology R&D.

Al Sandrock, MD

Thank you, Jim. Today I will be providing a number of updates on our pipeline with an emphasis on neurology, my area of responsibility. I will begin with our MS portfolio.

As we have said in the past our goal with MS is simple, but powerful, slow, stop and eventually reverse the disease. With AVONEX we have made major progress on slowing the disease. Based on a growing body of unprecedented efficacy data we believe TYSABRI goes a long way towards stopping disease activity in relapsing MS patients.

Let me start with a brief remark on the benefit TYSABRI brings to patients with relapsing MS. Every day we hear from physicians and patients about how TYSABRI has made a significant, positive, impact in their lives. They are corroborating the benefits that we have observed in our clinical studies on a wide array of measures of efficacy and quality of life. This drug was approved because it offers hope for many patients with this devastating disease.

I would also like to provide you with the recent updates on TYSABRI safety. As I mentioned before, TYSABRI is among the most intensely monitored drugs on the market today. We share and discuss these data with regulators around the world on an ongoing basis and work with them to keep healthcare providers up to date. Biogen Idec and our partner Elan currently believe, as the recent FDA update indicated, that the risk of developing PML increases with the number of TYSABRI infusions received. We continue to believe that the overall rate of developing PML with TYSABRI remains consistent with the rate implied on the label. We have proposed, and are currently discussing with the regulatory authorities, a potential label change to reflect this increased risk of PML with increased duration of TYSABRI exposure.

Stepping back, it is important to remember that PML remains a rare adverse event. Outcomes have been better than previously expected and we believe the overall benefit risk profile remains favorable. Real world patient and physician experience continue to establish TYSABRI as a compelling option for the treatment of MS bringing hope to many patients and transforming the care of MS patients.

Additionally, we continue to allocate significant time and resources to identifying PML risk factors and in developing ways to stratify, mitigate, and manage the risks. We are working on this internally and we are also working to set up a consortium of other interested collaborators. The premise of our work is that PML in TYSABRI treated patients’ results from a convergence of factors including the presence of JC virus, immune compromise, viral mutations, duration of treatment, and perhaps other factors such as risk [oleal] MFO.

With respect to the presence of virus recent published data in larger cohorts using more refined serological techniques indicates that seroprevalence is in fact less frequent in the textbook dogma of 80% or 90%. We have analytically validated a serological method with the goal of one day offering a commercially available assay that may inform about the relative risk of developing PML.

Now onto to some neurology pipeline updates. The neurology pipeline achieved some important milestones during the third quarter of 2009: I will start with Fampridine-SR.

This oral small molecule is a first in class selective blocker of voltage-gated potassium channels. It is thought to improve nerve conduction in demyelinated nerve fibers. Our partner, Acorda Therapeutics, met with an FDA advisory committee last Wednesday October 14. The advisory committee voted 12-1 that clinical data on Fampridine-SR 10 mg b.i.d. demonstrated substantial evidence of effectiveness as a treatment to improve walking in people with MS and voted 10-2 that this effect is clinically meaningful.

Next, I am happy to mention that in the third quarter we completed enrollment in CONFIRM, the second Phase III trial for BG-12, our oral compound for the treatment of relapsing, remitting MS. As you may recall DEFINE, the first Phase III trial, enrolled its last patient at the end of the first quarter of 2009. This is a significant accomplishment especially when considering the scope of the trials which involve more than 2,500 patients in over 25 countries.

Another MS program advancing is Daclizumab made by a high yield process which we call Daclizumab height, a humanized antibody that acts against the high affinity IL 2 receptors. During Q3 we and partner Facet Biotech made the decision to advance Daclizumab

to a Phase III trial. This was in part based on the results of the planned interim futility analysis of the ongoing SELECT study. An independent safety monitoring committee analyzed the subset of the data from this ongoing trial and recommended the continuation of the SELECT trial. SELECT remains a blinded study and will serve as one of the two trials for registration. We expect to start the Phase III trial during the first half of 2010.

On our Anti-LINGO program we have completed our GLP toxicology studies and remain on track to file a clinical trial application by the end of the year. The Anti-LINGO antibody has been shown to remyelinate nerve fibers in our animal studies and thus we hope it will help to reverse some of the damage done by diseases like multiple sclerosis.

In terms of other pipeline update there are some interesting developments going on there as well. In mid-September Roche announced positive data from the Phase III PRIMA study of RITUXAN in follicular lymphoma patients. The primary endpoint was progression free survival in patients receiving RITUXAN and standard chemotherapy followed by a maintenance schedule of RITUXAN mono therapy compared to patients with no maintenance treatment. The positive study was stopped early after a preplanned interim analysis and results will be presented in an upcoming scientific meeting.

Returning to RITUXAN in rheumatoid arthritis on October 16 the FDA issued a complete response to our sBLA seeking to extend the RITUXAN label to a broader DMARD-IR population. The FDA expressed concerns relating to the prolonged nature of RITUXAN mediated B cell depletion and the risk for TML in the less refractory RA population than our current label. We expect to meet with the FDA to discuss risk benefit for RITUXAN and then determine the appropriate next step. In the meantime RITUXAN remains an important therapy for TNS inadequate responder RA patients.

In the TNS IR population the FDA approved additional language to the label in October to clarify that patients being treated should receive subsequent courses every six months. Previously there was no guidance in the label on retreatment beyond the first course and the average retreatment interval has been seven to eight months. RITUXAN’s ability to improve physical function and slow joint damage for up to two years, as demonstrated in clinical studies, has also been added. Taken together this will allow new promotional messaging around lasting efficacy and regular dosing.

In addition there is regulatory concern about an apparent imbalance in opportunistic infections among Ocrelizumab treated RA and lupus patients in these clinical trials. Based on our recent safety review of Ocrelizumab data in RA and lupus nephritis clinical trials the Ocrelizumab film study in methotrexate naïve RA patients has been placed on clinical hold and dosing was stopped. We also decided to close the Ocrelizumab BELONG study in lupus nephritis. The other Ocrelizumab RA and relapsing remitting MS studies remain ongoing. We will work with regulators to determine the next step for these programs.

Next, in October, after a strategic review of programs we determined that the LUCID trial of lumiliximab and CLL and the target trial of Galiximab and NHL will not support registration. Accordingly we decided to stop recruitment in the lumiliximab LUCID trial and prematurely end the Galiximab target trial. Neither decision was a consequence of any safety concerns. We are evaluating our options for these programs and are working on a path forward.

On a more positive note we were pleased to announce yesterday, with partner Biovitrum, a positive read out on our Phase I/II study of our Factor IX for hemophilia B and plan to advance the program to a registrational trial in 2010. The trial was an open label, multi-center, safety dose escalation study that evaluated the safety and pharmacokinetics of recombinant Factor IX in severe, previously treated hemophilia B patients. We believe this compound could potentially improve the standard of care in hemophilia B which typically requires retreatment every two or three days. If our Factor IX trial meets its primary endpoint it may extend the interval between doses to once a week or longer.

We made recent progress on several other early stage programs as well. For example we started a Phase I trial of Neublastin for neuropathic pain, enrolled the first patient in a Phase I/II study of anti-IGF-1R in hepatocellular carcinoma and made progress on dose escalation in our Phase I studies of our anti-TWEAK antibody in RA and Anti-Cripto-DM4 toxin conjugated antibody in solid tumors. Our discovery and research efforts remain an important strength.

Finally data read outs expected by year-end include the Phase II study of the Ocrelizumab trial in relapsing, remitting MS. In addition, we expect to fully enroll two other proof of concept trials by the end of the year, our trial of BG-12 in RA and interferon beta in ulcerative colitis.

In conclusion, we continue to make progress on our pipeline and we look forward to continuing to update you on our progress in the quarters ahead.

With that, I will hand it over to our Chief Operating Officer, Bob Hamm.

Bob Hamm

Thanks Al. During the third quarter our global revenue was $1.1 billion, up 3% year-over-year. Third quarter RITUXAN US net sales were up 2% year-over-year to $670 million. RITUXAN

revenues on our P&L were $284 million, down 5% year-over-year with 6% growth in our Q3 US profit share offset by a 28% decline in international RITUXAN revenues as our x-US royalties continue to expire.

Our product revenues of $802 million grew 6% year-over-year with nearly flat AVONEX sales buoyed by a 21% year-over-year growth in the TYSABRI business. TYSABRI added approximately 1,000 net new patients per month during the third quarter and posted its second quarter in a row at a blockbuster run rate with Q3 in market sales at $282 million.

Turning to the RITUXAN CD20 franchise, a highly penetrated lymphoma market coupled with the general downward economic crusher meant slower revenue growth overall for RITUXAN in Q3. Units declined by 1% year-over-year. Price growth of 5% year-over-year was balanced by a 27% increase in discounts and allowances yielding an overall 2% year-over-year revenue growth. Operating profit outpaced revenue growth however, at 4% year-over-year, due in part to discipline in spending and improved margins during the quarter.

Front line adoption and maintenance use of RITUXAN remains steady for labeled oncology indications, those being diffuse large B cell and indolent follicular NHL. Biogen Idec and Genentech submitted two separate sBLA’s in May this year for the CLL8 study in previously untreated CLL and for the REACH study in previously treated CLL. Both sBLA’s were accepted and granted priority review status by the FDA with a PDUFA date in November of ’09. CLL launch planning activities are on track.

As Al mentioned Biogen Idec and our partner Genentech will discuss the PRIMA results with regulatory authorities worldwide for the possible update of the product label.

Moving to the globally neurology business, AVONEX $580 million in global revenue for Q3 is up 1% year-over-year with a run rate of over $2 billion and approximately $139,000 patients on therapy worldwide, AVONEX is a foundation of our market leading franchise in neurology.

US AVONEX revenue is up 8% versus prior year with price increases taken earlier in the year mitigating the underlying decline in unit volume of 8%. In the US we did see an increase in the number of patients in our Access Program as Paul will detail.

During the same period in international markets AVONEX revenue is down 8% with a 1% increase in unit volume offset by 9% decrease in net price largely due to foreign exchange. We believe the US market can perform better and have taken steps to improve that trajectory including our expansion earlier this year of the AVONEX field force and a change in leadership of the US business. We are confident that this is possible since we are holding our share of the ABCR market and are international markets and we see no reason why we can’t bring the same performance and results to the US. Approximately half of the US prescribers are now aware of the 10-year CHAMPIONS data which demonstrated sustained benefit over ten years of treating patients with AVONEX from their first MS attack. This is compelling data. Of physicians who have been exposed to it 1/3 have indicated they would increase their use of AVONEX in CIS patients and ¼ said they would also increase their use of AVONEX in relapse and remitting patients. AVONEX pioneered early treatment of MS and now with the CHAMPIONS 10-year follow-up data we demonstrated compelling, long-term benefit in patients treated after their first attack. The message is simple: AVONEX proven efficacy and best in class adherence demonstrates that AVONEX has the power to work early and keep patients active longer.

In addition, we are pleased to have our AVONEX method of use patent issued last month. The US patent covers the use of AVONEX for immunomodulation including the treatment of MS and extends to September 2026. The biosimilar pathway in the US, as we know, is still to be defined. Outside the US we continue to expect biosimilar competition, but we do not see evidence of clinical activity for any biosimilar competitors at this time.

Turning to TYSABRI, we had global end market revenues of $282 million in the third quarter, a 19% increase compared to the prior year with an over $1 billion run rate TYSABRI is the growth driver of our neurology franchise. We continue to see growth in the number of patients on TYSABRI with approximately 46,200 patients receiving TYSABRI at the end of September: of those approximately 13,400 patients have now been on therapy for over two years. During Q3 our estimate of the average weekly net new patient growth moderated somewhat driven by seasonality in x-US markets. In the US net weekly ad-in patients have continued to accelerate. Internationally our estimate of net weekly patient growth slowed somewhat from prior quarters. This was driven by seasonality in Europe during the summer holidays with lower net patient add- ins in July, and particularly August, followed by renewed strength in September which internationally was only down 7% from the prior quarter average.

We continue to work with the global neurology community to improve their confidence in using TYSABRI safely. For instance in Germany Biogen Idec has over the past 12 months partnered with a local neurology community to formalize relationships between more academic reference centers in many of the larger MS clinics so that TYSABRI prescribing can occur in a more structured environment and according to a common protocol developed and published by the Medical Advisory Board of German MS AOL’s. To date 250 top German MS treatment centers are linked to 40 reference centers.

We also continue to communicate with physicians about TYSABRI’s unprecedented efficacy and market research confirms that physician confidence with TYSABRI continues to improve. During the three months from June to August in the US TYSABRI became the No. 1 switch to therapy for the first time since the first half of ’08 with Copaxone patients being the primary source of switches.

We continue to strengthen TYSABRI’s efficacy position through physician awareness of data presented at this years ECTRIMS and AAN that demonstrates TYSABRI’s ability to provide many patients with freedom from disease activity as well as improvement in physical and mental disability. Based on this stream of evidence TYSABRI is changing the treatment paradigm from failure based to improvement based for MS patients.

Our newest program Fampridine-SR is progressing well. Biogen Idec is responsible for non-US development and commercialization of Fampridine. Regulatory filings are targeted in Canada by the end of this year and in Europe during the first quarter of 2010. The recent FDA Advisory Committee on October 14 underscored the burden that walking difficulty presents to MS patients and the importance of this new therapy. We hope Fampridine-SR will become the first oral therapy to show efficacy in improving walking ability of patients across the spectrum of MS disease space, including patients with secondary progressive MS and progressive MS for whom there has been previously no indicated treatment.

On another note, we are finally in the process of reviewing our manufacturing strategy. As many of you know we continually look at our biologics manufacturing capacity based on the projected volumes of our marketed program products, projected demand, and commercial potential from our clinical programs, process improvements, and other strategic considerations.

I will now turn the call over to our CFO Mr. Paul Clancy to walk you through Q3 financial statements.

Paul Clancy

Thanks Bob. Our results for the third quarter were in line with our full year operating plan. We are pleased with this performance, especially in the context of a number of challenges this quarter, including normal seasonality, a stronger dollar year-over-year, and reduced RITUXAN rest of world royalties.

The GAAP financials I provided in Tables 1 and 2 of the earnings release; Table 3 is a reconciliation of GAAP to non-GAAP financial results. Our Q3 GAAP diluted EPS was $0.95. Our Q3 non-GAAP diluted EPS was $1.12 an increase of 14% on a year-over-year basis. The primary differences between our GAAP and non-GAAP results for the quarter were $51 million related to the amortization of intangible assets, $8 million for employee stock option expense, and an offsetting $13 million impact related to those items. Our amortization of the AVONEX intangible asset was lower this quarter due to an increase in the expected lifetime revenue of AVONEX following the issuance of the 7-75 patents in the third quarter.

Now I will move onto the non-GAAP P&L operating performance of Biogen Idec which we believe better represents the economics of our business and reflects how we manage the business internally and set operational goals.

Q3 total revenue was $1,121,000,000.00 representing a 3% growth over the same period last year. Year-over-year growth was somewhat muted by foreign exchange which had a negative impact of approximately 4%.

Going through our product revenue I will begin with AVONEX. Q3 AVONEX worldwide product revenue was $580 million up 1% versus the same period last year. Q3 US AVONEX product revenue was $348 million representing an 8% increase versus last year. AVONEX units in the US declined approximately 8% which was offset by price increases.

In the US we did experience a continued increase in the number of patients supported by free drugs which we refer to as our Access Program. The impact from supporting Access patients accounted for approximately a 2% to 3% unit decline.

We ended Q3 in the US with approximately 2.2 weeks of inventory in the channel, down from 2.3 weeks in Q2.

Q3 international AVONEX product revenue was $232 million representing a decrease of 8% on a year-over-year basis. Remember Q3 2008 was a strong quarter due to the German wholesaler buy-ins which impacted the comparison this year resulting in a small year-over-year unit increase. The unfavorable FX impacted the year-on-year comparison by approximately $25 million on AVONEX international sales. Never the less, AVONEX gained share outside of the US in both a quarter-over-quarter basis and year-over-year basis.

Q3 TYSABRI worldwide Biogen Idec product sales were $207 million; a 21% increase versus Q3 2008 and 10% increase sequential quarter. End market sales were $282 million. More than three years after the relaunch TYSABRI continues to deliver double-digit growth on both a quarter-over-quarter and year-on-year basis.

US end user TYSABRI sales totaled $131 billion; we booked $59 million of this amount.

International TYSABRI sales totaled $148 million and this number is net of a $4 million currency hedge loss. Gross international TYSABRI sales totaled $151 million.

The total unfavorable impact of foreign exchange on AVONEX and TYSABRI versus Q3 2009 totaled approximately $37 million.

Now moving on to the RITUXAN collaboration revenues referred to as revenue from unconsolidated joint business: we recorded $2184 million in revenue for the quarter representing a decrease of 5% on a year-over-year basis. This is broken down to three components: First, our share of the net US RITUXAN profits. Net US RITUXIN sales were $670 million in the quarter up 2% versus prior year, and our Q3 profit share from that business was $203 million, up 6% versus prior year. Year-over-year we benefited from price increases and lower operating expenses in the collaboration.

Second, we received revenues on sales of Rituximab outside the US and in Q3 this was $65 million, down 28% versus prior year. This is driven by the continued expiration of rights to our royalties on a country-by-country basis outside the United States and Canada. For the majority of European countries the first commercial sale of RITUXIN occurred in the second half of 1998. We therefore expect a sequential decrease of royalty revenues moving into Q4 bringing this full year number to approximately $250 million.

Third, we were reimbursed $16 million for selling and developing costs incurred related to RITUXIN.

Q3 royalties for Biogen Idec were $35 million for the quarter.

Now I will turn to the expense lines on the P&L which include the non-GAAP adjustments that I described earlier.

Q3 cogs were $93 million representing 8% of revenues. On a year-over-year basis we witnessed a meaningful decline in cogs as a percentage of product revenue. Our manufacturing group has been successful in implementing operations excellence initiatives which has resulted in lower write offs and favorable production variances this year.

Q3 R&D expense was $299 million, a 13% increase on a year-over-year basis and approximately 27% of revenues. The drivers of this increase included a $20 million milestone payment to Cardiokine and the continued progression of our late stage pipeline with investments to support Lixivaptan, BG-12, the peg interferon program and Galiximab and lumiliximab.

Q3 SG&A expenses were $221 million representing 20% of revenues and a 2% decrease in overall spend versus prior year. The year-on-year decrease benefited from the strengthening dollar and G&A efficiencies.

Continuing down the P&L our collaboration profit sharing lines totaled $61 million in expense for the quarter. This represents our payment of 50% of profits outside the US to [align] and the reimbursement of third party royalties incurred by [align] outside the US.

Other income and expense for the quarter was a gain of approximately $9 million primarily driven by realized gains on the sale of marketable securities and strategic investments as we have de-risked our portfolio in a favorable environment.

Our Q3 non-GAAP tax rate was approximately 27.7%. The decrease in the third quarter non-GAAP tax rate was due to recognizing a 1x discrete benefit associated with certain of company charges and foreign related taxes in conjunction with filing our 2008 tax returns. This resulted in a favorable impact of approximately 160 basis points for the quarter.

We expect our Q4 non-GAAP tax rate to be approximately 30%. This brings us to Q3 non-GAAP diluted earnings per share if $1.12.

Our full year guidance is essentially in line with prior communication. Full year revenue growth is expected to be in the mid to high single digits on a year-over-year basis modestly changed. Operating expenses are unchanged with full year R&D expected to be between 28% to 30% of revenue and SG&A between 19% and 20%. This results in operating expenses, excluding collaboration profit share, to be between $2.1 and $2.2 billion.

The non-GAAP tax rate is expected to be between 28% and 30% for the full year and GAAP tax rate between 29% and 31% for the full year.

Non-GAAP diluted earnings per share are expected to be above $3.85, unchanged from prior communication.

GAAP diluted earnings per share are expected to be above $2.97 which now includes the favorable impact of lower amortization of intangible assets.

Our capital expenditure outlook for the full year is in the range of $150 to $160 million modestly lower.

This guidance excludes any significant business development activity in the fourth quarter.

So, Q3 kept us on course to achieve our 2009 full year operating plan as we drove operating margin improvement in the quarter and delivered 14% non-GAAP diluted earnings per share growth.

Lastly, I would like to provide some detail on the share repurchase program Jim alluded to in his opening comments.

You may recall that Biogen Idec has a 20 million share repurchase authorization which was authorized by the board in October 2006. This program has approximately 6 million shares remaining and has been and will be used for annual share stabilization. Over the last few months we have carefully reviewed three key factors that heavily influence the deployment of capital: namely our access to credit and the health of the financial markets, the landscape for M&A transaction, and the underlying cash flow generation of the Company. With all of these factors in mind Biogen Idec’s Board of Directors has recently authorized an additional repurchase of up to $1 billion of common stock. This $1 billion authorization is intended to reduce our shares outstanding with the objective of returning excess cash to shareholders. Repurchase stock in this authorization will be retired, the authorization is open ended and shares will be purchased on the open market.

The repurchase reflects our confidence in the long-term value of our common stock and we believe is an effective way of returning cash to our shareholders. We believe this strikes the right balance in our corporate finance strategy. We are confident in the projected cash flows from our core products such that we can return capital to shareholders while continuing to fund future growth through our pipeline.

We continue to review acquisitions and external growth opportunities and believe we have the cash flow and financing capacity to capitalize on potential opportunities. We will update you on the progress of his stock repurchase program on future earnings calls.

I will now turn the call over to Jim for his closing comments.

Jim Mullen

Thanks, Paul and I will be brief because we have a lot of information this quarter and we should get to Q&A.

In summary business performance and pipeline progress for the quarter was very good. We believe that the strong fundamentals of the business across all products and geographies will continue to deliver robust results and create significant value for our shareholders.

With that, Eric, let’s open this up for Q&A.

Question-and-Answer Session

Operator

(Operator Instructions) Your first question comes from Eric Schmidt with Cowen And Company.

Eric Schmidt - Cowen And Company

My question is on the opportunistic infections that Al mentioned regarding Ocrelizumab. I am just looking for a little bit more information. What type of infections did you see, have you observed these in the past with RITUXAN and why isn’t the ongoing MS trial impacted?

Al Sandrock, MD

That is a lot of questions. We are not commenting on the types of opportunistic infections. I can say that we saw a lot of these predominantly in Asia and the reason for the imbalance right now is unknown.

In terms of the Ocrelizumab our MS trial, while it is a different indication, you know the unmet need is different and that trial is actually over in terms of the efficacy read out portion, and in fact we plan to be looking at some data later this year.

Operator

Your next question comes from Joel Sendek with Lazard Capital Markets

Joel Sendek - Lazard Capital Markets

I have a question about Fampridine-SR. It looks to me that you are targeting a little bit earlier filing time than you previously stated and I am wondering what is left on the critical path to that filing, and if you could tell us at all about what kind of meetings you have had with the European regulators about the one point that the Company had.

Al Sandrock, MD

I think the main issue that we had to grapple with was the requirement for a pediatric plan which we have had some verbal interactions with the MEA, and we have a verbal agreement on a plan forward. That was the main issue that we dealt with, and yes we are planning to file in early 2010.

Operator

Your next question comes from May-Kin Ho with Goldman Sachs.

May-Kin Ho - Goldman Sachs

You mentioned that you have been talking with the FDA about changing the label on TYSABRI in terms of the higher risk of PML when you have long duration of therapy. Will you be specifying how long patients should be treated and what kind of changes are you thinking about?

Al Sandrock, MD

We are not specifying how long they should be treated, in fact there is not going to be any mention of terminating treatment. The overall risks are still within the rate implied in the label currently. The main reason that we are implementing this label change is predominantly so that our labels worldwide are roughly harmonized in terms of what it says about duration. In some locales our label stated that the link with duration was unknown and clearly that is not compatible with our current thinking, so that was the main reason for asking for a label change. In terms of the overall risk benefit we believe it remains favorable and nothing major has changes. In fact we think that the risk is basically the same as that implied in the label currently.

May-Kin Ho - Goldman Sachs

Will you have to spell out what the risks are at different time periods?

Al Sandrock, MD

We are still in discussions with the regulators at this point.

Operator

Your next question comes from Geoff Meecham with J.P. Morgan.

Geoff Meecham - J.P. Morgan

I have a follow up question to the last question. With respect to the label change for TYSABRI how often will you guys update the label and then what do you think would be the FDA or the MEA consequences should one of the longer duration groups exceed the 1/1000 rate?

Al Sandrock, MD

It is difficult to speculate on those things. I mean the frequency of updating the label will be determined by the change in information that we see as more knowledge is gathered.

Operator

Your next question comes from Geoffrey Porges with Sanford Bernstein.

Geoffrey Porges - Sanford Bernstein

Back up to TYSABRI for a second, you did give us some incremental information about Galiximab and lumiliximab; I am wondering if you could give us a sense of how much that could potentially reduce your R&D spend in the future if those programs are not continued. How much of the 27% you are spending now would come out and could we see sort of incremental savings to R&D next year?

Paul Clancy

I would say we are right in the middle of it, so not totally prepared. It is 2-0 right now, kind of two out of six or seven of our large pivotal trials, so it does have an impact as we kind of roll into next year. We do want to make sure you are mindful of the fact that this thing isn’t necessarily turned off automatically. We will kind of look at the path forward, but I think as we spin into next year and the next earnings call we will be able to give you a lot better visibility as it relates to that impact.

Operator

Your next question comes from Mark Schoenebaum with Deutsche Bank Securities.

Mark Schoenebaum - Deutsche Bank Securities

Paul, you guys do have 2007 through 2010 longer-term guidance out there from a top line and bottom line perspective. Are you still comfortable with that and can you actually give the market shares for AVONEX in the US and Europe?

Paul Clancy

I wouldn’t use this call to kind of address anything on or off of that. What I would remind you is that those were a set of goals in totality. They actually had product goals, pipeline goals and financial goals. As we have been around on investor conferences I think we have tried to be clear that some of those goals were on track; some of those goals were far exceeding, particularly on the pipeline front, and some of those goals were kind of falling short of the TYSABRI patient goals obviously. In the totality, in the spirit of those goals that we set up, we still are certainly going after those for the 2007 to 2010 time period.

Operator

Your next question comes from Josh Schimmer with Leerink Swann.

Josh Schimmer - Leerink Swann

I was curious about the commentary regarding a commercially available assay for relative risk of PML in TYSABRI. Were you referring to the JC virus assay or is there any interest in returning to the Cylex Assay to better quantify the immune system function? The last update I think you were less enthusiastic for that assay but I am wondering if you now have more hope.

Al Sandrock, MD

Actually I was referring to the anti-JCV assay.

Josh Schimmer - Leerink Swann

Is there any interest in returning to the Cylex or other immune quantification type assays to screen patients, has that changed or evolved?

Bob Hamm

We are very interested in assessing immune function. We will continue to look at whatever data come out from Cylex. We are also working on assays related to CD8 response to VC-1.

Operator

Your next question comes from Yaron Werber with Citi.

Yaron Werber - Citi

On BG-12 which is actually a pretty interesting drug just given some of the issues on safety from the oral drugs out there, are you going to release the 52-week data from the find and from CONFIRM or are we going to have to wait until the 104-week data?

Bob Hamm

Both of these trials are full two-year trials and our goal is to complete these trials before looking at or announcing data.

Operator

Your next question comes from Jason Zhang with BMO Capital Market.

Jason Zhang - BMO Capital Market

You made a comment about assessing your manufacturing capacity. Does that mean you will have excess capacity? If that is a yes is that excess capacity the result of an increase of skill or is it actually a result of lower revenue projection?

Jim Mullen

It is actually a combination of a number of factors. The first and the biggest impact is simply the high side process for TYSABRI that got approved which is almost 4x as productive as the previous commercial process. While that approval was earlier in the year, we are into that process now. I think the other factors are just you drop things like LT beta out of the pipelines, and maybe some of the other protein products there is probably a little less pressure near-term on commercial capacity.

Having said all of that, I think people always have to be mindful of backup capacity, so that we have dual sourcing for key programs. That was one of the primary reasons for cross licensing both the Cambridge and RTP facilities as well as having a second large-scale facility. However, having said all of that, I think we believe we have a certainly sufficient capacity and probably too much capacity over the next couple of years at large scale.

Operator

Your next question comes from Jim Birchenough with Barclays Capital.

Jim Birchenough - Barclays Capital

I was wondering if you could provide an update on the methacycline treatment study in terms of when you would expect data from that study at this point and related to that there is a one log imbalance at baseline it seems between treatment and control and if you get the 40 patients enrolled and you still have that imbalance what do you do at that point?

Al Sandrock, MD

Well we would adjust for that imbalance cyclically and we expect to see data toward the end of next year.

Operator

Your next question comes from Christopher Raymond with Robert W. Baird & Co., Inc.

Christopher Raymond - Robert W. Baird & Co., Inc.

I have a general question on AVONEX. Jim you alluded to a loss of US market share, can you maybe talk about what the drivers of that might be? Is that increased competitive activity or maybe some change of effort on your part? Without giving anything away can you talk about what specifically you are going to do to change that dynamic?

Jim Mullen

Well, I mean certainly it is increased competitiveness, but a lot of it comes back to old-fashioned marketing and messages and discipline around that. What we are looking to do and what Bob is looking to do is improve and tighten up our marketing message and deliver it in a consistent fashion much as we have done in the international markets, which has proven to be a good strategy. The other thing is you can start to look more regionally or almost more specifically center-by-center to think about how you tailor some of these messages more to the individual centers, the individual regions, which sometimes has slightly different dynamics.

Eric Hoffman

To follow up on the AVONEX market share in the US and x-US, in the US AVONEX’s market share of the ABCR market is in the range of 30%, just a tick above; x-US AVONEX’s market share in the ABCR market is around 27%.

Operator

Your next question comes from Steven Harr with Morgan Stanley

Steven Harr - Morgan Stanley

I wanted to get an understanding, previously you guys have said that you did not believe that TYSABRI PML risk was related to time on the drug and then clearly something changed. You gave us exposure numbers, is there something new on number of PML cases you can offer us, or is there something you can offer us as an explanation as to why you saw more patients exposed to the drug during the quarter than on therapy? It must have been 1,300 patients that dropped off during the course of the quarter.

Bob Hamm

You know we are not giving out actual patient numbers, but I can tell you as time goes on the numbers of patients treated for the longer duration is increased and our 95% competence intervals on the incident rate narrows and as that happens we get more clarity about the risk. That was the reason why we had decided to update the label with this increase in the risk with the length of exposure.

Operator

Your next question comes from Eun Yang with Jefferies & Co.

Eun Yang - Jefferies & Co.

We heard recently from your [inaudible] that there were a few more cases of PML and so the number of cases around that are around 17. With that said there seems to be an indication between the duration of TYSABRI treatment and PML cases and some doc’s tended to focus on the longer duration therapy, so when you look at the patients who have been on the treatment for 24-months or longer PML rate runs around 1 in 800 which is higher than what is in the label currently. So, my question to you is what do you think would be the critical threshold of a PML rate that where physicians or regulatory agencies would become more cautious on TYSABRI?

Bob Hamm

I don’t want to speculate what makes regulators want to do things, but I can assure you that our current thinking is that the risk of PML even in that third year beyond 24-months is within the currently implied risk in the label.

Operator

Your next question comes from Michael Aberman of Credit Suisse.

Michael Aberman - Credit Suisse

I have a follow up question to that in some regards. In Europe you saw a slow down in sales and you are accounting primarily the seasonality; however we know that a number of new PML cases came from there and you are instituting changes in Germany to try to rectify, I guess, a situation where there is perhaps less control. I am wondering if you can just expand on what you have seen in the marketplace in terms of Europeans perception about risk and explain in more detail what you are doing in Germany to counter that.

Bob Hamm

Well actually at this time, as I said, seasonality we think accounted for July, August, and September actually bounced back quite nicely including levels in Germany we hadn’t seen for three months or so. So, I think the German authorities and the KOLs there that are working with us have taken a very responsible approach and just making sure that appropriate use of TYSABRI is monitored and followed up with, but there is no sign that they don’t think anything other than this is a risk-benefit matter and that the benefit certainly outweighs the risk.

Operator

Your next question comes from Maged Shenouda with UBS.

Maged Shenouda - UBS

Can you just elaborate a little bit on patient churn with TYSABRI or even compliance? Are you seeing any changes since the FDA’s recent commentary on PML risk?

Bob Hamm

No, we aren’t seeing that. We did see that about a year or so ago with the first cases, but thus far we are really not seeing any reaction to other information discussions ongoing.

Operator

Your next question comes from Rachel McMahon with Banc of America Securities.

Rachel McMahon - Banc of America Securities

On TYSABRI can you talk about what proportion of patients in your database are implementing drug holidays, how long a holiday might be, and when you calculate your patients, if a patient misses two doses are you still considering them to be on drug?

Al Sandrock, MD

From the data we have we are seeing very, very isolated cases of that. We are really not seeing anything more than physician practices that have been in place probably for a year, so no there has not been any real change in that regard.

Operator

Your next question comes from Geoffrey Porges with Sanford Bernstein.

Geoffrey Porges - Sanford Bernstein

I have some follow up R&D questions; one is on BG-12. Do you have any ideas when you might be in a position to start a combination study or will you have to get the full two-year data from the ongoing Phase III? Then on the Factor IX, during a pivotal trial is there any sense of whether you might initiate a pivotal trial for comparable Factor VIII program?

Al Sandrock, MD

Let me take that last question first. The Factor VIII IND has been submitted in Q3 as we had planned and we are waiting for feedback on that, so we are very excited about that program as well and we hope to initiate Phase I trials with that soon after we hear the FDA feedback.

In terms of BG-12 we are very interested in combination therapy. We do not feel we need to complete the Stage III program before we start work on combination therapy and our plan is to initiate combination work as early as early next year.

Operator

Your next question comes from Geoff Meecham from J.P. Morgan.

Geoff Meecham - J.P. Morgan

I have a bigger picture question for Jim, with Al’s updates to the pipeline today and the developments with [Identry] you guys have a little bit less late stage pipeline assets and I am wondering what this share repurchase says about your willingness to do deals to backflow the pipeline?

Jim Mullen

I think as Paul tried to explain, what I thought was relatively clearly, we did go through the process of looking across the M&A landscape, our cash flows and what the financing markets are and we think there has been a market change in the financing market than access to capital. So, our willingness to do deals is certainly not, I wouldn’t take any signal from the share buyback of our willingness to do deals. I think we are being pragmatic about what is out there in fact and we are going to continue to be very active on the PD front with an emphasis to things that are late stage programs.

Operator

Your next question comes from Jim Birchenough from Barclays Capital.

Jim Birchenough - Barclays Capital

I just want to tie up a lose end, a number of 17 confirmed PML cases was put forward. Is that the number that you are familiar with and when will we get a formal update from the Company on PML cases next?

Jim Mullen

I think as we have said previously we aren’t going to be giving everybody the count by count to the extent we do update that, that will be in the context of medical meetings. What we will discuss are things like we discussed today, things that are meaningful to either what is going on in the marketplace or the label. I think that is probably a more appropriate way to really discuss the risk/benefit of the compound going forward.

Operator

Your last question comes from Yaron Werber with Citi.

Yaron Werber - Citi

Paul, I have one quick question on amortization and one on the guidance. On the amortization of acquired intangible assets it was a big drop off this quarter and you did mention that, is that sustainable going forwards and into the out years? Secondly just on the share buyback, can you give us a sense as to is this something you want to get done over the next few months, or is this something that is now going to get done over the long term? Because if you look at your guidance for Q4 I am surprised you are not raising it further, because you have already done $293 and you are easily on track to do more than $4.00 this year, so I am just trying to understand what is going on here.

Paul Clancy

The amortization which affects the GAAP P&L, not the non-GAAP P&L, every year we will, as per kind of our accounting policy, revisit the economic useful life of that asset. That asset was put on the books when the Biogen and Idec merger came together. With the issuance of the 775 patents the lifetime revenue of AVONEX is projected to be a bit more durable than it was in the past year. We do anticipate that the run rate that you saw in Q3 will be the run rate for that amortization plus or minus in Q4 and spinning into 2010. Then, as per our policy we will continue to look at that useful life on an annual basis, call it a year from now.

With respect to the share buyback timing, in my comments I kind of said that it was open ended, so we expect to do it in a very thoughtful, diligent way, trying to capitalize on low points in the stock price within the guidelines from a 10B 18 perspective. It won’t have a meaningful impact even if we are very aggressive in the fourth quarter, it just won’t have a meaningful impact because of the way the share counts are counted for 2010.

Eric Hoffman

Thank you very much for your participation in today’s call.

Operator

Ladies and gentlemen that does conclude the conference call for today. We thank you for your participation. (Operator Instructions)

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Source: Biogen Idec Inc. Q3 2009 Earnings Call Transcript
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