UNITED STATES
SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-K/A

AMENDMENT NO. 1 TO FORM 10-K

(Mark one)

For the fiscal year ended December 31, 2008

For the transition period from                to

Commission file number   000-30941

AXCELIS TECHNOLOGIES, INC.

(Exact name of registrant as specified in its charter)

108 Cherry Hill Drive
Beverly, Massachusetts 01915

(Address of principal executive offices, including zip code)

(978) 787-4000

(Registrant’s telephone number, including area code)

Securities registered pursuant to Section 12(b) of the Act:

Securities registered pursuant to Section 12(g) of the Act:

Common Stock, $0.001 par value
Preferred Share Purchase Rights

Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act.  Yes o  No  x

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act.  Yes o  No  x

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15 (d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.  Yes x  No  o

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of registrant’s knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K. x

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See definitions of “large accelerated filer,” “accelerated filer,” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Act).  Yes o  No x

Aggregate market value of the voting stock held by non-affiliates of the registrant as of June 30, 2008: $497,275,221.

Number of shares outstanding of the registrant’s Common Stock, $0.001 par value, as of March 27, 2009: 103,283,850.

Documents incorporated by reference:

Portions of the definitive Proxy Statement for Axcelis Technologies, Inc.’s Annual Meeting of Stockholders held on May 1, 2008 are incorporated by reference into Part III of this Form 10-K.

AMENDMENT NO. 1

EXPLANATORY NOTE

We are filing this amendment to our Annual Report on Form 10-K for the fiscal year ended December 31, 2008 originally filed with the Commission on March 31, 2009 (the “Original 2008 Form 10-K”). This amendment to our Annual Report on Form 10-K for the fiscal year ended December 31, 2008 supplements Item 15 (Exhibits, Financial Statement Schedules), which was filed with our original 2008 Form 10-K. This Form 10-K/A files the financial statements of SEN Corporation, an SHI and Axcelis Company (“SEN”) as of March 31, 2008 and 2007 and the related financial statements for each of the three years in the period ended March 31, 2008 (the “SEN Financial Statements”). The SEN Financial Statements were previously filed under a Form 10-K/A on September 29, 2008 and have been updated for this filing with Note 17 on Subsequent Events regarding the Company’s sale of its shares in SEN, the entry into a License Agreement with SEN on March 30, 2009, and the termination of arbitration between Axcelis and SEN.

Item 15. Exhibits, Financial Statement Schedules

(a) The following documents are filed as part of the Company’s Form 10-K, as originally filed on March 31, 2009, and as amended by this form 10-K/A:

(1)(A) Financial Statements of Axcelis Technologies, Inc.:

Report of Independent Registered Public Accounting Firm

Consolidated Statements of Operations — For the years ended December 31, 2008, 2007 and 2006

Consolidated Balance Sheets — December 31, 2008 and 2007

Consolidated Statements of Stockholders’ Equity — For the years ended December 31, 2008, 2007 and 2006

Consolidated Statements of Cash Flows — For the years ended December 31, 2008, 2007 and 2006

Notes to Consolidated Financial Statements

(1)(B) Financial Statements of SEN Corporation, an SHI and Axcelis Company:

Report of Independent Auditors

Consolidated Statements of Income — For the years ended March 31, 2006, 2007 and 2008

Consolidated Balance Sheets — March 31, 2007 and 2008

Consolidated Statements of Stockholders’ Equity — For the years ended March 31, 2006, 2007 and 2008

Consolidated Statements of Cash Flows — For the years ended March 31, 2006, 2007 and 2008

(2) Financial Statement Schedules:

Schedule II — Valuation and Qualifying Accounts for the years ended December 31, 2008, 2007 and 2006

All other schedules for which provision is made in the applicable regulation of the Securities and Exchange Commission are not required under the related instructions or are inapplicable, and therefore have been omitted.

(b) Exhibits

The exhibits filed as part of this Form 10-K are listed on the Exhibit Index immediately preceding such Exhibits, which Exhibit Index is incorporated herein by reference.

(c) Financial Statement Schedules

The response to this portion of Item 15 is submitted as a separate section of this report.

Consolidated Financial Statements

As of March 31, 2007 and 2008 and
for the years ended March 31, 2006, 2007 and 2008

Contents

Report of Independent Auditors

The Board of Directors

SEN Corporation, an SHI and Axcelis Company

We have audited the accompanying consolidated balance sheets of SEN Corporation, an SHI and Axcelis Company (the “Company”) as of March 31, 2008 and 2007, and the related consolidated statements of income, shareholders’ equity, and cash flows for each of the three years in the period ended March 31, 2008, all expressed in Japanese yen.  These financial statements are the responsibility of the Company’s management.  Our responsibility is to express an opinion on these financial statements based on our audits.

We conducted our audits in accordance with auditing standards generally accepted in the United States.  Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement.  We were not engaged to perform an audit of the Company’s internal control over financial reporting.  Our audits included consideration of internal control over financial reporting as a basis for designing audit procedures that are appropriate in the circumstances, but not for the purpose of expressing an opinion on the effectiveness of the Company’s internal control over financial reporting.  Accordingly, we express no such opinion.  An audit also includes examining, on a test basis, evidence supporting the amounts and disclosures in the financial statements, assessing the accounting principles used and significant estimates made by management, and evaluating the overall financial statement presentation.  We believe that our audits provide a reasonable basis for our opinion.

In our opinion the financial statements referred to above present fairly, in all material respects, the consolidated financial position of the Company, at March 31, 2008 and 2007, and the consolidated results of its operations and cash flows for each of the three years in the period ended March 31, 2008, in conformity with generally accepted accounting principles in the United States.

As discussed in Note 10 to the consolidated financial statements, the Company adopted the recognition provisions of Statement of Financial Accounting Standards No. 158, Employers’ Accounting for Defined Benefit Pension and Other Postretirement Plans - An Amendment of FASB Statements No. 87, 88, 106 and 132(R) effective on March 31, 2008.

We also have recomputed the translation of the consolidated financial statements as of and for the year ended March 31, 2008 into United States dollars.  In our opinion, the consolidated financial statements expressed in Japanese yen have been translated into United States dollars on the basis described in Note 2.

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SEN Corporation, an SHI and Axcelis Company

Consolidated Statements of Income

See accompanying notes to consolidated financial statements.

2

SEN Corporation, an SHI and Axcelis Company

Consolidated Balance Sheets

See accompanying notes to consolidated financial statements.

3

SEN Corporation, an SHI and Axcelis Company

Consolidated Statements of Shareholders’ Equity

See accompanying notes to consolidated financial statements.

4

SEN Corporation, an SHI and Axcelis Company

Consolidated Statements of Cash Flows

See accompanying notes to consolidated financial statements.

5

SEN Corporation, an SHI and Axcelis Company

Notes to Consolidated Financial Statements

Note 1.  Nature of Business and Significant Accounting Policies

General

SEN Corporation, an SHI and Axcelis Company (the “Company”), was established on April 1, 1983 under the Commercial Code of Japan.  The Company is owned equally by Sumitomo Heavy Industries, Ltd. (“SHI”), a Japanese corporation, and Axcelis Technologies, Inc. (“Axcelis”), a U.S. corporation.  The Company designs, manufactures, sells and repairs ion implantation equipment and semiconductor equipment primarily for semiconductor manufacturing customers.

On April 1, 2006, the Company changed its name from “Sumitomo Eaton Nova Corporation” to “SEN Corporation, an SHI and Axcelis Company.”

Basis of Presentation

The Company and its subsidiary maintain their books of account in conformity with the accounting principles generally accepted in Japan.  The consolidated financial statements of the Company and its subsidiary presented herein have been prepared in a manner and reflect the adjustments which are necessary to conform them with accounting principles generally accepted in the United States of America (“U.S.”).

Principle of Consolidation

The consolidated financial statements include the accounts of the Company and its wholly-owned subsidiary located in Japan.  All significant intercompany balances and transactions are eliminated in consolidation.

Use of Estimates

The preparation of consolidated financial statements in conformity with generally accepted accounting principles in the U.S. requires management to make certain estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of revenues and expenses during the reporting period.  The actual results could differ from those estimates.

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SEN Corporation, an SHI and Axcelis Company

Notes to Consolidated Financial Statements (continued)

Note 1.  Nature of Business and Significant Accounting Policies (continued)

Foreign Currency

Transaction gains and losses, which arise from transactions denominated in a currency other than the Japanese yen, are included in non-operating income (expenses).  Transaction gains and losses in each of the years in the three year period ended March 31, 2008 were not material.

Cash Equivalents

All highly liquid investments with a maturity of three months or less when purchased are considered to be cash equivalents.

Inventories

Inventories are stated at the lower of cost or market.  The cost of raw material inventories is determined on the average cost method.  The cost for work in process inventories are determined based on the specific identification method.

Property, Plant and Equipment

Property, plant and equipment is carried at cost less accumulated depreciation.  Depreciation is computed using the declining-balance method over the estimated useful lives of the respective assets (buildings — 6 to 40 years; machinery — 5 to 15 years; and furniture, fixtures and automobiles — 2 to 20 years) except for buildings purchased after April 1, 1998, which are depreciated on the straight-line basis over 31 years.

Impairment of Long-Lived Assets

Long-lived assets are reviewed for impairment losses whenever events or changes in circumstances indicate the carrying amount may not be recoverable.  Recoverability of assets to be held and used would be considered impaired when the net undiscounted future cash flows generated by the assets are less than their carrying value.  An impairment loss would be recognized based on the amount by which the carrying value of the asset exceeds its fair value. Assets to be disposed of by sale are reported at the lower of the carrying amount or fair value less costs to sell, and are no longer depreciated.

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SEN Corporation, an SHI and Axcelis Company

Notes to Consolidated Financial Statements (continued)

Note 1.  Nature of Business and Significant Accounting Policies (continued)

Income Taxes

Deferred tax assets and liabilities are recognized for the estimated future tax consequences attributable to differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases and operating loss and tax credit carryforwards. Deferred tax assets and liabilities are measured using enacted tax rates expected to apply to taxable income in the years in which those temporary differences are expected to be recovered or settled. The effect on deferred tax assets and liabilities of a change in tax rates are recognized in the period in which they are enacted. The Company records a valuation allowance to reduce the deferred tax assets to the amount that is more likely than not realizable.

The Company adopted the provisions of Financial Accounting Standards Board (“FASB”) Interpretation No. 48, Accounting for Uncertainty in Income Taxes, an interpretation of FASB Statement No. 109 on April 1, 2007.  Upon adoption, the Company recognizes the financial statement effects of tax positions when it is more likely than not, based on the technical merits, that the tax positions will be sustained upon examination by the tax authorities. Benefits from tax positions that meet the more-likely-than-not recognition threshold are measured at the largest amount of benefit that is greater than 50 percent likely of being realized upon settlement. Interest and penalties accrued related to unrecognized tax benefits are included in income taxes in the consolidated statements of income.

Revenue Recognition

In general, the Company recognizes revenue when there is persuasive evidence of an arrangement, delivery has occurred or the services have been rendered, the sales price is fixed or determinable and collection of the related receivable is reasonably assured.

When a sales arrangement involves multiple elements, the items included in the arrangement (deliverables) are evaluated to determine whether they represent separate units of accounting.  The arrangement consideration is allocated to the individual items based on their relative fair values.  If there is objective and reliable evidence of fair value of the undelivered item in an arrangement, but no such evidence for the delivered item, the residual method is used to allocate the arrangement consideration.

Absent objective and reliable evidence of fair value for the undelivered item in a multiple-element arrangement, the Company combines all deliverables into a single unit of accounting, and recognizes revenue when the last item has been delivered and all revenue recognition criteria applicable to the last delivered item has been met.

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SEN Corporation, an SHI and Axcelis Company

Notes to Consolidated Financial Statements (continued)

Note 1.  Nature of Business and Significant Accounting Policies (continued)

Revenue Recognition (continued)

For domestic equipment sales that require installation services, the Company recognizes revenue upon customers’ acceptance.  For export equipment sales, revenue is recognized when title and risk of loss transfers to the customer, generally upon shipment.  When the final payment is subject to customer acceptance, a portion of revenue for the final payment is deferred until an enforceable claim has become effective.

Service revenue includes revenue from spare parts, maintenance services and equipment overhaul services.  Revenue related to maintenance service contracts is recognized ratably over the duration of the contracts.  Revenue related to services and equipment overhauls is recognized upon completion and acceptance of the service.  Revenue related to services and equipment overhauls is recognized upon the later of shipment or when title and risk of loss passes to the customer.

Taxes collected from customers and remitted to governmental authorities are excluded from revenues in the consolidated statements of income.

Shipping and Handling Costs

Shipping and handling costs are included in cost of products sold.

Research and Development Costs

Research and development costs are expensed in the year in which such costs are incurred.

Reclassifications

Certain prior year amounts have been reclassified to conform to the current year presentation.

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SEN Corporation, an SHI and Axcelis Company

Notes to Consolidated Financial Statements (continued)

Note 1.  Nature of Business and Significant Accounting Policies (continued)

Recent Accounting Pronouncements

In September 2006, the FASB issued Statement of Financial Accounting Standard (“SFAS”) No. 157, Fair Value Measurements (“SFAS 157”). SFAS 157 defines fair value, establishes a framework for measuring fair value, and expands disclosures about fair value measurements. SFAS 157 is effective for fiscal years beginning after November 15, 2007 and is required to be adopted by the Company in the fiscal year beginning after April 1, 2008. In February 2008, the FASB issued Staff Positions No. FAS 157-1, Application of FASB Statement No. 157 to FASB Statement No. 13 and Other Accounting Pronouncements That Address Fair Value Measurements for Purposes of Lease Classification or Measurement under Statement 13 and No. FAS 157-2, Effective Date of FASB Statement No. 157, which partially delay the effective date of SFAS 157 for one year for certain nonfinancial assets and liabilities and remove certain leasing transactions from its scope. The adoption of SFAS 157 will not have a material impact on the Company’s consolidated results of operations and financial condition.

In September 2006, the Financial Accounting Standards Board (“FASB”) issued Statement of Financial Accounting Standard No. 158, Employers’ Accounting for Defined Benefit Pension and Other Postretirement Plans-An Amendment of FASB Statements No. 87, 88, 106, and 132R (“SFAS 158”).  SFAS 158 requires an employer to recognize the funded status of pension and other postretirement benefit plans on sponsoring employers’ balance sheets and to recognize changes in the funded status in comprehensive income in the year the changes occur. It also requires the measurement date of plan assets and obligations to be at the end of the employers’ fiscal year. The Company adopted the requirement to recognize the funded status of its benefit plan and the disclosure requirements in its financial statements as of and for the year ending March 31, 2008, as described in Note 10 Employees’ and Directors’ Retirement Benefits.  However, the requirement to measure plan assets and benefit obligations as of the date of the employer’s fiscal year-end consolidated balance sheet shall be effective for the Company’s fiscal year ending March 31, 2009.  Adoption of the measurement date provisions of SFAS 158 will require the Company to record adjustments to retained earnings and accumulated other comprehensive income for the effect of net periodic benefit costs incurred in the period January 1, 2008 to March 31, 2008.  The Company is currently evaluating whether to re-measure plan assets and benefit obligations as of March 31, 2008 to determine the effects of the measurement date change at March 31, 2008 (re-measurement method) or to continue to use the measurements as of December 31, 2007 and report the estimated effects of the measurement date change by allocating three-fifteenths of the net periodic benefit cost determined for the period from December 31, 2007 to March 31, 2009 (alternative method).  As a result, the impact of applying the measurement date provisions has yet to be determined.

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SEN Corporation, an SHI and Axcelis Company

Notes to Consolidated Financial Statements (continued)

Note 2.  Basis of Financial Statement Translation

The accompanying consolidated financial statements expressed in yen, solely for the convenience of the reader, have been translated into United States dollars at the rate of ¥100.19 per US$ 1, the approximate exchange rate prevailing on the Tokyo Foreign Exchange Market as of March 31, 2008.  This translation should not be construed as a representation that all amounts shown could be converted into U.S. dollars.

Note 3.  Trade Receivables

The components of trade receivables at March 31, 2007 and 2008 were as follows:

Note 4.  Inventories

The components of inventories at March 31, 2007 and 2008 were as follows:

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SEN Corporation, an SHI and Axcelis Company

Notes to Consolidated Financial Statements (continued)

Note 5.  Property, Plant and Equipment

The components of property, plant and equipment at March 31, 2007 and 2008 were as follows:

Note 6.  Product Warranty

The Company offers a one year warranty for all its products, the terms and conditions of which vary depending upon the product sold.  The Company estimates the costs that may be incurred under its warranty and records a liability in the amount of such costs at the time product revenue is recognized.  Factors that affect the Company’s warranty include the number of installed units, historical and anticipated product failure rates, material usage and service labor costs.  The Company periodically assesses the adequacy of its recorded warranty and adjusts the amount as necessary.

Changes in the Company’s product warranty (included in other current liabilities on the consolidated balance sheets) for the years ended March 31, 2006, 2007 and 2008 are as follows:

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SEN Corporation, an SHI and Axcelis Company

Notes to Consolidated Financial Statements (continued)

Note 7.  Transactions with Affiliates

Transactions with affiliates for the years ended March 31, 2006, 2007 and 2008 were as follows:

The sales and purchase transactions with SHI, Axcelis, and their affiliates have been conducted at cost plus a fixed rate of 12%-25%.

The royalties to Axcelis were charged to the Company at 3.5% - 5.5% of net sales. The sales commissions to Axcelis were charged to the Company at 10% of net sales. The rates for both royalty and sales commission are specified in the master license agreement entered into between the Company and Axcelis.

13

SEN Corporation, an SHI and Axcelis Company

Notes to Consolidated Financial Statements (continued)

Note 7.  Transactions with Affiliates (continued)

The management fees and royalties to SHI were charged to the Company at 1% of net sales, which is specified in the management fee agreement.

The Company earned profits of ¥58,617 thousand, ¥80,009 thousand, and ¥53,677 thousand (US$ 535 thousand) in 2006, 2007 and 2008, respectively, on revenue recognized from sales to Axcelis and affiliates, none of which have been eliminated in consolidation.

Balances due from and to affiliates at March 31, 2007 and 2008 were as follows:

Pension funding for seconded employees (employees on temporary assignment) is provided through a plan administered by SHI.  Under this arrangement, the Company is billed monthly for the pension costs attributable to those individuals.  Under the terms of the pension agreement with SHI, no additional costs related to earned benefits are to be borne by the Company.  Pension contributions paid to SHI for the years ended March 31, 2006, 2007 and 2008 were ¥126,977 thousand, ¥91,026 thousand and ¥78,236 thousand (US$ 781 thousand), respectively.

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SEN Corporation, an SHI and Axcelis Company

Notes to Consolidated Financial Statements (continued)

Note 8. Leases

Rental expenses for equipment, land and office space for the years ended March 31, 2006, 2007 and 2008 amounted to ¥266,976 thousand, ¥257,467 thousand and ¥253,515 thousand (US$ 2,530 thousand), respectively.  Future minimum non-cancelable rental commitments at March 31, 2008 under operating leases are as follows:

Note 9.  Income Taxes

Income taxes include corporation, enterprise, and inhabitants’ taxes which, in the aggregate, resulted in a statutory tax rate of approximately 40.44% in 2006, 2007 and 2008.  The difference between the provision for income tax and the amount computed by applying the statutory income tax rate in effect for the year ended March 31, 2006, 2007 and 2008 resulted from nondeductible expenses, tax credits for costs of information technologies, research and development activities, and other miscellaneous items. The 2008 provision for income taxes also includes a credit related to the true up of 2007 income taxes.