Income Taxes

6 Months Ended

Jun. 30, 2011

Income Taxes [Abstract]

Income Taxes

16.   Income Taxes

For the three and six months ended June 30, 2011, our effective tax rate was 23.8% and 25.7%, respectively, compared to 25.8% and 25.7%, respectively, in the prior year comparative periods.

The decrease in our tax rate for the three and six months ended June 30, 2011, compared to the same periods in 2010, was primarily due to an increase in research and development expenditures eligible for the orphan drug credit and a lower effective state tax rate resulting from a change in state law, offset by a higher percentage of our 2011 profits being earned in higher tax rate jurisdictions, principally the U.S. In addition, our effective tax rate was favorably impacted by the settlement of an outstanding IRS audit matter in the first quarter of 2011.

Reconciliation between the U.S. federal statutory tax rate and our effective tax rate is summarized as follows:

	For the Three Months						For the Six Months
	Ended June 30,						Ended June 30,
	2011			2010			2011			2010
Statutory rate		35.0	%		35.0	%		35.0	%		35.0	%
State taxes		0.4			1.9			1.4			1.9
Taxes on foreign earnings		(7.3	)		(10.3	)		(6.3	)		(10.1	)
Credits and net operating loss utilization		(4.1	)		(1.6	)		(3.1	)		(1.6	)
Purchased intangible assets		1.4			1.5			1.4			1.5
IPR&D		—			0.8			—			0.8
Permanent items		(1.1	)		(1.7	)		(1.2	)		(1.7	)
Other		(0.5	)		0.2			(1.5	)		(0.1	)
Effective tax rate		23.8	%		25.8	%		25.7	%		25.7	%

Accounting for Uncertainty in Income Taxes

We and our subsidiaries are routinely examined by various taxing authorities. We file income tax returns in the U.S. federal jurisdiction, and various states and foreign jurisdictions. With few exceptions, we are no longer subject to U.S. federal tax examination for years before 2007 or state, local, or non-U.S. income tax examinations by tax authorities for years before 2001. During the second quarter of 2011, we adjusted our unrecognized tax benefits to reflect new information arising during our ongoing audit examinations.

Contingencies

In 2006, the Massachusetts Department of Revenue (DOR) issued a Notice of Assessment against Biogen Idec MA Inc. (BIMA), one of our wholly-owned subsidiaries, for $38.9 million of corporate excise tax for 2002, which includes associated interest and penalties. The assessment asserts that the portion of sales attributable to Massachusetts (sales factor), the computation of BIMA’s research and development credits and certain deductions claimed by BIMA were not appropriate, resulting in unpaid taxes for 2002. We filed an abatement application with the DOR seeking abatement for 2001, 2002 and 2003. Our abatement application was denied and on July 25, 2007 we filed a petition with the Massachusetts Appellate Tax Board (the Massachusetts ATB) seeking, among other items, abatements of corporate excise tax for 2001, 2002 and 2003 and adjustments in certain credits and credit carryforwards for 2001, 2002 and 2003. Issues before the Massachusetts ATB include the computation of BIMA’s sales factor for 2001, 2002 and 2003, computation of BIMA’s research credits for those same years, and the availability of deductions for certain expenses and partnership flow-through items. The hearing on our petition has been stayed by the Massachusetts ATB to allow the parties to discuss a negotiated resolution of all disputes as to 2001, 2002 and 2003. The Massachusetts ATB has ordered a status conference for September 6, 2011, at which the parties will report on the status of the settlement discussions. If a negotiated resolution is concluded, we do not expect it to have a significant impact on our financial position or results of operations. We have and will continue to evaluate the facts, circumstances and information available in accordance with our financial reporting policies to reflect management’s best estimate of the outcome. Based upon our most recent estimates, we currently expect to settle this matter in exchange for a payment of $7.0 million in taxes, plus interest, and expect to reach an agreement on the tax credits carried forward into 2004.

On June 8, 2010, we received Notices of Assessment from the DOR against BIMA for $103.5 million of corporate excise tax, including associated interest and penalties, related to our 2004, 2005 and 2006 tax filings. We believe the asserted basis for these assessments is consistent with that for 2002. Assessments related to periods under dispute, including associated interest and penalties, total $142.4 million. We filed an abatement application with the DOR seeking abatement for 2004, 2005 and 2006. Our abatement application was denied and we filed a petition appealing the denial with the ATB on February 3, 2011. For all periods under dispute, we believe that positions taken in our tax filings are valid and believe that we have meritorious defenses in these disputes. We are contesting these matters vigorously.

Our tax filings for 2007 and 2008 have not yet been audited by the DOR but have been prepared in a manner consistent with prior filings which may result in an assessment for those years. Due to tax law changes effective January 1, 2009, the computation and deductions at issue in previous tax filings have not been part of our tax filings in Massachusetts starting in 2009.

We believe that these assessments do not impact the level of liabilities for income tax contingencies. However, there is a possibility that we may not prevail in defending all of our assertions with the DOR. If these matters are resolved unfavorably in the future, the resolution could have a material adverse impact on the effective tax rate and our results of operations.