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Isis Reports Financial Results and Highlights for Third Quarter 2010
Date:11/4/2010

051)Reconciliation of GAAP to Pro Forma BasisAs illustrated in the Selected Financial Information in this press release, pro forma operating expenses and pro forma income (loss) from operations were adjusted from GAAP to exclude compensation expense related to stock options, which are non-cash.  Isis has regularly reported non-GAAP measures for operating expenses and income (loss) from operations as pro forma results.  These measures are provided as supplementary information and are not a substitute for financial measures calculated in accordance with GAAP.  Isis reports these pro forma results to better enable financial statement users to assess and compare its historical performance and project its future operating results and cash flows.  Further, the presentation of Isis' pro forma results is consistent with how Isis' management internally evaluates the performance of its operations.

Isis Pharmaceuticals, Inc.Condensed Consolidated Balance Sheets(In Thousands)September 30,December 31,20102009(unaudited)Assets:  Cash, cash equivalents and short-term investments$497,904$574,312  Other current assets9,64621,814  Property, plant and equipment, net35,54927,338  Other assets32,75933,720Total assets$575,858$657,184Liabilities and stockholders' equity:  Other current liabilities$23,648$35,763  Current portion of deferred contract revenue77,26875,681  2 5/8% convertible subordinated notes130,882125,100  Long-term obligations, less current portion14,45111,478  Investment in Regulus Therapeutics Inc.5,000-  Long-term deferred contract revenue70,900107,097  Stockholders' equity253,709302,065Total liabilities and stockholders' equity$575,858$657,184
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