Cautionary Note Regarding Forward-Looking Statements

This Quarterly Report on Form 10-Q and certain information incorporated herein by reference contain forward-looking statements within the "safe harbor" provisions of the Private Securities Litigation Reform Act of 1995. All statements included or incorporated by reference in this Quarterly Report, other than statements that are purely historical, are forward-looking statements. Words such as "anticipate," "expect," "intend," "plan," "believe," "seek," "estimate," "could," "may," and similar expressions also identify forward-looking statements. The forward-looking statements include, without limitation:

• Our belief that the impairment related to auction-rate securities is temporary, our intent to not sell our auction-rate securities, our belief that we will not be required to sell our auction-rate securities before recovery, our expectation to recover the amortized cost of our auction-rate securities, and our belief that we will ultimately be able to liquidate our investments in auction-rate securities without significant loss through successful auctions, redemptions of securities by the issuers or upon maturity;

• Our anticipation to reclassify the accumulated loss recorded as of September 26, 2009 for cash flow hedges from OCI to net sales within twelve months;

• Our expectation that the adoption of certain accounting pronouncements will not have a significant impact on our Condensed Consolidated Financial Statements;

• Our estimated amortization expense for currently recognized identifiable intangible assets for the fourth quarter of 2009 and for the years ending December 31, 2010, 2011, 2012, 2013 and 2014, respectively;

• Our expectation that the remaining obligations in connection with vacated facilities will be satisfied no later than the expiration dates of the lease terms, which expire on various dates through 2017;

• Our expectation that the ultimate disposition of the Linear litigation and other litigation matters that have arisen, or may arise in the future, in the normal course of business will not have a material adverse effect on our business, financial condition or operating results;

• Our expectation that in years 2011 and beyond our income subject to tax in California will be lower, our expectation that our deferred tax assets are less likely to be realized due to the recent California tax law change, our plan to continue to assess our tax valuation allowance on our California deferred tax assets in future periods, and our belief that our year-to-date tax provision for income taxes is the most reliable estimate of our annual effective income tax rate;

• Our expectation that of the $22.4 million of unrecognized compensation cost related to unvested stock options, $4.0 million is expected to be recognized in the fourth quarter of 2009, and $11.5 million, $4.9 million and $2.0 million is expected to be recognized in 2010, 2011 and 2012, respectively;

• Our expectation that of the $22.2 million of unrecognized compensation cost related to restricted stock awards, $3.3 million is expected to be recognized in the fourth quarter of 2009 and $8.9 million, $7.3 million, $2.6 million and $0.1 million will be recognized in 2010, 2011, 2012 and 2013, respectively;

• Our belief that significant investment in research and development is required to remain competitive, our plan to continue to invest in new products and enhance our current product lines, and our belief that our continued investment in research and development has positioned us for future growth;

• Our belief that our operations will continue to be increasingly impacted by the prime wafer industry, which is characterized by intense competition and rapidly changing technology;

• Our intention to continue to seek legal protection through patents and trade secrets for our proprietary technology;

• Our intent to continue to work closely with our customers and make substantial investments in research and development in order to deliver innovative products which enhance productivity for our customers to utilize the latest technology;

• Our expectation that chip unit growth will resume in 2010 and beyond, and with it, spending on semiconductor equipment;

• Our expectation that we will incur additional costs related to consolidating our manufacturing operations in our Tualatin, Oregon facility;

• Our expectation that net orders will fluctuate due to the cyclicality of the semiconductor industry;

• Our plan for continued focus on operational execution and paring down our cost structure to improve operating results;

• Our belief that operating expenses will increase if we were to return to profitability;

• Our belief that all of our net deferred tax assets will be realized;

• Our belief that our current cash position and available borrowing capacity will be sufficient to meet our needs through the next twelve months;

• Our belief that sales of our products to relatively few customers will continue to account for a high percentage of our net sales in the foreseeable future;

• Our expectation that we will continue to experience significant fluctuations in our quarterly operating results;

• Our intention to use the proceeds from certain credit agreements for working capital and other general corporate purposes, including the repurchase of shares; and our intention to repurchase shares from time to time in the open market, through block purchases or otherwise; and

• Our belief that future impairment charges related to goodwill or long-lived assets may be required if our future operating results do not meet current forecasts or if we have a sustained decline in our market capitalization that is determined to be indicative of a reduction in fair value of one or more of our reporting units.

Our expectations, beliefs, objectives, intentions and strategies regarding the future, including, without limitation, those concerning expected operating results, revenues and earnings and current and potential litigation are not guarantees of future performance and are subject to risks and uncertainties that could cause actual results to differ materially from results contemplated by our forward-looking statements. These risks and uncertainties include, but are not limited to:

• Unanticipated trends with respect to the cyclicality of the semiconductor industry;

• Our inability to reclassify the accumulated loss for our cash flow hedges from OCI to net sales within twelve months;

• Inaccuracies regarding growth potential in the Asia region over the long term;

• A sustained decrease in or leveling off of customer demand;

• Our inability to make adequate inventory valuation adjustments in a timely manner;

• Our inability to manage inventory levels;

• Unexpected changes in the tax regulatory environment, changes in accounting and tax standards or practices, and our inability to achieve a tax benefit due to unexpected changes in domestic tax regulations;

• Our inability to predict the ultimate outcome of the Linear litigation and other current litigation on our business, financial conditions or operating results;

• Our inability to accurately predict the impact of new accounting pronouncements on our Condensed Consolidated Financial Statements;

• Our inability to accurately assess the period in which we will recognize unrecognized compensation related to unvested stock options and restricted stock awards;

• Inaccuracies related to the timing and satisfaction of remaining obligations related to vacated leases;

• Unexpected shipment delays which adversely impact shipment volumes;

• Our inability to meet certain performance conditions that may result in forfeiture of certain restricted stock awards;

• Unexpected increase in costs associated with manufacturing our products; our inability to anticipate cyclical changes in customers' capacity utilization and demand; the negative impact of higher cost of services on gross margins;

• Our inability to realize efficiencies from outsourcing; inefficiencies in the allocation of funds towards our research and development efforts to our existing and new product lines;

• Unexpected complications related to timing, success and cost of our manufacturing consolidation efforts;

• Unexpected difficulties in introducing new and enhanced products in a timely manner in order to remain competitive;

• Unexpected changing product needs of our customers, the loss of major customers, and the need to seek new customers and diversify our customer base;

• Our inability to enforce our patents and protect our trade secrets;

• Our inability to recover the amortized cost of our investments in auction-rate securities, market changes negatively affecting auction-rate securities and the government's inability to guarantee the underlying securities;

• Our inability to accurately predict customers capital spending over the long term;

• Further periodic downturns in the semiconductor industry which could have a material adverse effect on the semiconductor industry's demand for semiconductor processing equipment;

• Our inability to accurately predict mega-fabrication trends in memory manufacturing and uncertainties related to the acceptance of new technology into the memory market;

• The introduction of new products by competitors;

• Our inability to gain and leverage market position during the economic downturn;

• Unexpected shifts in market demands for both memory and logic products; and

• Uncertainties related to growth in the electronic industry and our inability to successfully select, develop, and market new products, or enhance existing products.

The forward-looking statements in this Quarterly Report on Form 10-Q are subject to additional risks and uncertainties set forth under the heading "Risk Factors" in Item 1A of Part II, and are based on information available to us on the date hereof. We assume no obligation to update any forward-looking statements. Readers are cautioned not to place undue reliance on forward-looking statements, which speak only as of the date of the filing of this Quarterly Report on Form 10-Q. Readers should also review carefully the cautionary statements and risk factors listed in our Annual Report on Form 10-K for the year ended December 31, 2008 and in our other filings with the SEC, including our Forms 10-Q and 8-K and our Annual Report to Shareholders.

Introduction

The following Management's Discussion and Analysis of Financial Condition and Results of Operations (MD&A) is intended to provide readers with an understanding of our business. The following are included in our MD&A:

• Overview of our Business and Industry;

• Critical Accounting Policies;

• Results of Operations; and

• Liquidity and Capital Resources.

Overview of Our Business and Industry

Novellus Systems, Inc. is a California corporation organized in 1984. At Novellus, we primarily develop, manufacture, sell and support equipment used in the fabrication of integrated circuits, commonly called chips or semiconductors. Customers for these products manufacture chips for sale or for incorporation in their own products, or provide chip-manufacturing services to third parties. The segment of our business serving this area is the Semiconductor Group. Beginning in 2004, Novellus entered into market segments beyond semiconductor manufacturing through various acquisitions. The segment we refer to as our Industrial Applications Group develops, manufactures, sells and supports grinding, lapping and polishing equipment for fine-surface optimization and serves a broad spectrum of industrial applications.

In the Semiconductor Group our business depends on capital expenditures made by integrated circuit manufacturers, who in turn are dependent on corporate and consumer demand for integrated circuits and the electronic products which use them. Since the industry in which we operate is driven by spending for electronic products, our business is directly affected by growth or contraction in the global economy as well as by the adoption of new technologies. Demand for personal computers, the expansion of the Internet and telecommunications industries and the emergence of new applications in consumer electronics have a direct impact on our business. In addition, the industry is characterized by intense competition and rapidly changing technology. We continue to work closely with our customers and make substantial investments in research and development in order to deliver innovative products which enhance productivity for our customers and utilize the latest technology. We believe these investments have positioned us for future growth.

In the Industrial Applications Group our business depends on capital expenditures made by manufacturers in sectors such as automotive, aircraft and electronic products, parts and components. At the broadest level, the demand for machine tools is highly sensitive to macroeconomic conditions, as our customer base includes some of the most cyclically sensitive industries in the economy. As a result, such variables as the outlook for overall economic growth, fixed investment and durable goods shipments directly affect the growth of our business. Our industrial business also depends on niche applications in addition to the general machine tool cycle. As we continue to expand our capabilities in this segment, our operations are increasingly impacted by the prime wafer industry which, similar to the semiconductor segment, is also characterized by intense competition and rapidly changing technology.

As a supplier to the global semiconductor and semiconductor-related industries, we are subject to business cycles and trends which are difficult to predict. The demand for our products is affected by the profitability of our customers which is driven by capacity and the market supply-demand balance for their products. Our customers operate principally in the semiconductor memory and logic markets. In fiscal 2006 and 2007, our memory customers grew capacity and those capacity additions outpaced the rate of demand, leading to declines in the average selling price of memory chips. This oversupply-driven weakness in the memory markets was rendered more severe in the second half of 2008 and the first half of 2009 by the contraction in demand for semiconductors due to the global economic crisis. Semiconductor sales have rebounded strongly in recent months, leading to a resumption in capacity additions by our customers; however, semiconductor and semiconductor capital equipment sales are still expected to decline year-over-year in 2009. While we can provide no assurances, in keeping with the historical cyclical nature of the industry, we generally expect chip unit growth to resume in 2010 and beyond, and with it, spending on semiconductor equipment.

Given the significant downward pressure on revenues over the past two years, we continue to focus on operational execution and paring down our cost structure to improve operating results. We plan to continue managing both our variable and fixed cost structure with the objective of maximizing cash flow from operations, including the consolidation of buildings at our San Jose, California campus. However, if we were to return to profitability we would expect an increase in variable compensation. In July 2009 we announced our plans to consolidate manufacturing in our Tualatin, Oregon facility by the end of 2009 at an incremental cost of $6 million to $10 million. In the third quarter of 2009, we incurred $3.0 million in additional charges, of which $1.2 million related to our manufacturing consolidation efforts and the remaining $1.8 million were primarily due to other reductions in workforce. Of these charges, $1.2 million was in cost of sales, $0.9 million was in selling, general and administrative expenses, $0.6 million was in research and development expenses and $0.3 million was in restructuring charges.

We focus on certain key quarterly financial data to manage our business. Net sales, gross profit, net income and net income per share are the primary measures we use to monitor performance. We also use certain non-GAAP measures, such as shipments and net orders, to assess business trends and performance. Shipments consist of products shipped to customers, without regard to net sales adjustments such as deferrals associated with customer acceptance. Net orders, which are also referred to as bookings, consist of current period orders less current period cancellations and other adjustments. Net orders reported for the third quarter of 2009, the second quarter of 2009, the first quarter of 2009 and the fourth quarter of 2008 were reduced by $12.3 million, $8.0 million, $10.6 million and $44.9 million, respectively, due to customer cancellations and backlog adjustments based upon our assessment that certain customers may not be in a financial position to take delivery within the next 12 months. Shipments and net orders are used to forecast and plan future operations. We do not report orders for systems with delivery dates more than 12 months from the latest balance sheet date.

The following table sets forth certain quarterly financial information for the periods indicated (in thousands, except per share data and percentages):

                                                                                        Quarterly Financial Data
                                                              2009                                                         2008
                                             Third           Second           First            Fourth             Third            Second             First
                                            Quarter          Quarter         Quarter           Quarter           Quarter           Quarter           Quarter
Net sales                                 $   176,879      $   119,208      $   98,913       $   188,453       $   250,098       $   257,740       $   314,713
Gross profit                              $    70,708      $    31,006      $   25,738       $    68,517       $   111,524       $   110,963       $   144,940
Net income (loss)                         $    (4,026 )    $   (50,008 )    $  (66,392 )     $  (130,251 )     $     1,397       $    (2,385 )     $    15,529
Net income (loss) per share - Diluted     $     (0.04 )    $     (0.52 )    $    (0.69 )     $     (1.36 )     $      0.01       $     (0.02 )     $      0.15
Shipments                                 $   165,446      $   119,982      $   92,130       $   175,635       $   230,153       $   240,319       $   312,857
Change in shipments from prior quarter             38 %             30 %           (48 )%            (24 )%             (4 )%            (23 )%            (14 )%
Net orders                                $   171,548      $   111,187      $   77,795       $    82,695       $   202,765       $   234,628       $   297,025
Change in net orders from prior quarter            54 %             43 %            (6 )%            (59 )%            (14 )%            (21 )%            (13 )%

We expect that net orders will continue to fluctuate due to the cyclical nature of our industry. The receipt of net orders in a particular quarter affects revenue in subsequent quarters. Net orders result in revenue either at shipment and transfer of title or upon customer acceptance of the equipment. Our revenue recognition policy, as discussed in our Annual Report on Form 10-K for the year ended December 31, 2008, addresses the distinction between the revenue recognized upon shipment and transfer of title and the revenue recognized upon customer acceptance. Equipment is generally shipped within two to nine months of receiving the related order and, if applicable, customer acceptance is typically received one to nine months after shipment. These time lines are general estimates and actual times may vary depending on various circumstances.

Critical Accounting Policies

The preparation of financial statements in conformity with U.S. GAAP requires that we make estimates and judgments that affect the reported amounts of assets, liabilities, revenues and expenses and the related disclosure of contingent assets and liabilities. On an ongoing basis, we evaluate our assumptions and estimates, including those related to recognition of revenue, valuation of inventory, valuation of goodwill and other intangible assets, valuation of deferred tax assets, adequacy of warranty obligations, measurement of restructuring and impairment charges, compliance with hedge accounting for derivatives, measurement of stock-based compensation expense, valuation of investments, adequacy of the allowance for doubtful accounts and adequacy of loss contingencies, including those related to legal matters. We base our estimates on historical experience and on various assumptions that are believed to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. Actual results may differ from these estimates under different assumptions or conditions. We discuss our critical accounting policies in Management's Discussion and Analysis of Financial Condition and Results of Operations in our Annual Report on Form 10-K for the year ended December 31, 2008. Except for the critical accounting policy set forth below entitled "Income Taxes" and "Goodwill," there have been no significant changes in our critical accounting policies or estimates since those reported in our Annual Report.

Income Taxes

Because our projected tax rate is unusually volatile, the provision for income taxes in our Condensed Consolidated Statements of Operations reflects our actual effective tax rate for the three and nine months ended September 26, 2009. We believe our year-to-date tax provision for income taxes is the most reliable estimate of our effective tax rate for the year. The effective income tax rate for the full fiscal year will likely be different from the tax rate in effect for the three and nine months ended September 26, 2009 and could be considerably higher or lower, depending largely on our operating results before taxes and the geographic mix of income (loss) for the year. Our future effective income tax rate also depends on other factors, such as tax legislation, non-deductible expenses incurred in connection with acquisitions and other discretely recorded items, including interest expense on uncertain tax positions and deductions for compensation expense related to stock options and restricted stock.

As of September 26, 2009, we had $112.7 million of net deferred tax assets. We currently believe all of our net deferred tax assets will be realized due to anticipated future income and our ability to carry back losses to prior years. We have considered all sources of taxable income and ongoing prudent and feasible tax planning strategies in assessing the need for the valuation allowance. If, in the future, we determine that we will not be able to realize all or part of our net deferred tax assets, a valuation allowance for deferred tax assets would decrease income in the period in which such determination is made. If market conditions change significantly within the next 12 months then it is reasonably possible that our valuation allowance will change.

Goodwill and Other Intangible Assets

We review our long-lived assets, including goodwill and other intangible assets, for impairment at least annually or whenever events or changes in circumstances indicate that the carrying amount of these assets may not be recoverable. In accordance with our policy, we perform our goodwill impairment test in the fourth quarter of each fiscal year separately for each of our reporting units. We define reporting units as the individual segments we operate. The first step of the test identifies if potential impairment may have occurred, while the second step measures the amount of the impairment, if any. Impairment is present when the carrying amount of net assets exceeds the fair value estimated during the first step of our annual goodwill impairment test. The estimation of the fair value of each reporting unit is determined based upon data generated from a discounted cash flow model, known as the income approach, and a comparable market price model, known as the market approach. The income approach requires us to make a number of assumptions including future growth rates, expense trends and working capital turnover ratios for each reporting unit over an extended period of time. Although the assumptions we utilize are consistent with the assumptions used to generate our annual strategic plan, there is significant judgment in the timing and level of future cash flows attributable to each reporting unit.

Our annual impairment test in the fourth quarter of 2008 resulted in a non-cash impairment charge within our Industrial Applications Group. The fair value of our Semiconductor Group marginally exceeded book value, which indicated that no impairment was present for this reporting unit. As of March 28, 2009 our expectations of future operating results for both reporting units declined from those used to perform our 2008 annual impairment test. This fact, in conjunction with the results of the fourth quarter 2008 annual impairment test, led us to determine that an indicator of potential impairment existed and that an interim impairment test was required. After completing the first step of the interim impairment test, we determined that the estimated fair value of each reporting unit exceeded its carrying value and as a result, no additional impairment charges were recorded. The fair value of our Industrial Applications Group exceeded its book value of $42.6 million by 44% in the first step of the impairment test performed as of March 28, 2009. No indicators of impairment were present during the second and third quarters of 2009. Given the relatively low fair value of this reporting unit, our impairment analysis is highly sensitive to slight changes in assumptions to our valuation model. As a result, we believe it is reasonably possible that our Industrial Applications Group could fail the first step in our annual impairment test to be completed in the fourth quarter of 2009. This analysis will be completed in conjunction with our update of the expected operating performance for each unit as part of our annual strategic planning process.

If our future operating results do not meet current forecasts or if we have a sustained decline in our market capitalization that is determined to be indicative of a reduction in fair value of one or more of our reporting units, future impairment charges related to goodwill or long-lived assets for both of our reporting units may be required. As of September 26, 2009, the carrying amounts of goodwill on our Consolidated Balance Sheet subject to impairment are $108.4 million and $18.5 million for the Semiconductor Group and Industrial Applications Group, respectively. We amortize our intangible assets with definite lives on a straight-line basis over their estimated useful lives.

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