Hologic (HOLX) 10-K 24 Nov 09 2009 FY Annual report Financial data

Statement Of Financial Position

Statement Of Financial Position Classified (USD $)
In Thousands	12 Months Ended Sep. 26, 2009	12 Months Ended Sep. 27, 2008
Current assets:
Cash and cash equivalents	$293,186	$95,661
Restricted cash	916	3,629
Accounts receivable, less reserves of $7,279 and $6,326 respectively	263,231	321,299
Inventories	182,780	174,667
Deferred income tax assets	52,165	53,660
Prepaid income taxes	172	17,797
Prepaid expenses and other current assets	29,066	26,865
Total current assets	821,516	693,578
Property and equipment, at cost:
Land	8,983	8,978
Buildings and improvements	57,214	55,743
Equipment and software	187,961	172,789
Equipment under customer usage agreements	125,635	100,316
Furniture and fixtures	11,112	11,083
Leasehold improvements	39,701	38,620
Property, Plant and Equipment, Gross, Total	430,606	387,529
Less-accumulated depreciation and amortization	158,978	103,554
Property, Plant and Equipment, Net, Total	271,628	283,975
Intangible assets, net (Note 2)	2,424,812	2,629,651
Goodwill	2,108,963	4,450,496
Other assets	62,909	76,932
Total assets	5,689,828	8,134,632
Current liabilities:
Current portion of long-term debt	38,373	38,480
Accounts payable	46,589	59,590
Accrued expenses (Note 14)	137,284	154,746
Deferred revenue	97,544	78,559
Deferred gain (Note 4)	9,500	9,500
Total current liabilities	329,290	340,875
Long-term debt, net of current portion (Note 5)	139,955	437,420
Convertible notes (Note 5)	1,725,000	1,725,000
Deferred income tax liabilities	912,970	920,838
Deferred service obligations-long-term	11,364	10,777
Other long-term liabilities (Note 14)	58,534	57,453
Commitments and contingencies (Notes 12 and 15)	-	-
Stockholders' equity
Preferred stock, $0.01 par value-1,623 shares authorized; 0 shares issued	0	0
Common stock, $0.01 par value-750,000 shares authorized; 257,938 and 256,373 shares issued, respectively	2,579	2,564
Capital in excess of par value	4,898,422	4,853,837
Accumulated deficit	(2,393,881)	(217,644)
Accumulated other comprehensive income	7,028	4,945
Treasury stock, at cost-214 shares	(1,433)	(1,433)
Total stockholders' equity	2,512,715	4,642,269
Total liabilities and stockholders' equity	$5,689,828	$8,134,632

1_Statement Of Financial Positi

Statement Of Financial Position Classified (Parenthetical) (USD $)
In Thousands, except Per Share data	Sep. 26, 2009	Sep. 27, 2008
Accounts receivable, reserves	$7,279	$6,326
Preferred stock, par value	0.01	0.01
Preferred stock, shares authorized	1,623	1,623
Preferred stock, shares issued	0	0
Common stock, par value	0.01	0.01
Common stock, shares authorized	750,000	750,000
Common stock, shares issued	257,938	256,373
Treasury stock, shares	214	214

Statement Of Income Alternative

Statement Of Income Alternative (USD $)
In Thousands, except Per Share data	12 Months Ended Sep. 26, 2009	12 Months Ended Sep. 27, 2008	12 Months Ended Sep. 29, 2007
Revenues:
Product sales	$1,426,986	$1,502,447	$628,854
Service and other revenues	210,148	172,052	109,514
Revenues, Total	1,637,134	1,674,499	738,368
Costs and expenses:
Cost of product sales	470,295	535,082	267,470
Cost of product sales-amortization of intangible assets	155,519	95,310	11,262
Cost of product sales-impairment of intangible assets	4,065	0	0
Cost of service and other revenues	149,769	151,589	114,307
Research and development	94,328	81,421	44,381
Selling and marketing	238,977	261,524	85,520
General and administrative	148,825	147,405	62,092
Amortization of intangible assets	51,210	25,227	5,584
Impairment of goodwill (Note 2)	2,340,023	0	0
Impairment of intangible assets (Note 2)	0	2,900	0
Acquired in-process research and development (Note 3)	0	565,200	0
Restructuring charges (Note 2)	797	6,383	0
Costs and Expenses, Total	3,653,808	1,872,041	590,616
(Loss) income from operations	(2,016,674)	(197,542)	147,752
Interest income	1,161	4,528	2,815
Interest expense	(69,502)	(84,912)	(2,511)
Other (expense) income, net	(3,660)	(1,215)	433
(Loss) income before income taxes	(2,088,675)	(279,141)	148,489
Provision for income taxes	87,562	106,476	53,911
Net (loss) income	($2,176,237)	($385,617)	$94,578
Basic net (loss) income per common share	-8.48	-1.57	0.88
Diluted net (loss) income per common share	-8.48	-1.57	0.86
Weighted average number of common shares outstanding:
Basic	256,545	245,968	106,873
Diluted	256,545	245,968	109,669

Statement Of Shareholders Equit

Statement Of Shareholders Equity And Other Comprehensive Income (USD $)
In Thousands		Common Stock Par Value	Capital in Excess of Par Value	Accumulated Deficit	Accumulated Other Comprehensive Income (Loss)		Treasury Stock Amount	Total
Beginning Balance at Sep. 30, 2006		$1,053	$531,728	$73,875	($442)		($464)	$605,750
Beginning Balance at Sep. 30, 2006	105,290					180
Issuance of common stock related to acquisitions	2,315
Issuance of common stock related to acquisitions		23	63,155					63,178
Exercise of stock options	2,695
Exercise of stock options		27	10,564					10,591
Stock-based compensation expense			6,104					6,104
Purchase of treasury shares to settle minimum withholding taxes						34
Purchase of treasury shares to settle minimum withholding taxes							(969)	(969)
Tax benefit related to exercise of stock options			21,926					21,926
Net income				94,578				94,578
Translation adjustments					2,353			2,353
Adjustment to minimum pension liability, net					2,212			2,212
Ending Balance at Sep. 29, 2007	110,300					214
Ending Balance at Sep. 29, 2007		1,103	633,477	168,453	4,123		(1,433)	805,723
Issuance of common stock related to acquisitions	132,060
Issuance of common stock related to acquisitions		1,321	3,670,818					3,672,139
Exercise of stock options	11,398
Exercise of stock options		114	170,995					171,109
Fair value of common stock issued in connection with conversion of Cytyc convertible debt	2,557
Fair value of common stock issued in connection with conversion of Cytyc convertible debt		25	84,176					84,201
Fair value of vested options exchanged related to acquisitions			256,941					256,941
Issuance of common stock to employees upon vesting of restricted stock units, net of minimum tax withholdings	58
Issuance of common stock to employees upon vesting of restricted stock units, net of minimum tax withholdings		1	(1,343)					(1,342)
Stock-based compensation expense			25,664					25,664
Tax benefit related to exercise of stock options			13,109					13,109
Cumulative effect of a change in accounting principle-FIN 48				(480)				(480)
Net income				(385,617)				(385,617)
Translation adjustments					1,092			1,092
Adjustment to minimum pension liability, net					(270)			(270)
Ending Balance at Sep. 27, 2008	256,373					214
Ending Balance at Sep. 27, 2008		2,564	4,853,837	(217,644)	4,945		(1,433)	4,642,269
Exercise of stock options	1,306
Exercise of stock options		13	9,379					9,392
Issuance of common stock to employees upon vesting of restricted stock units, net of minimum tax withholdings	138
Issuance of common stock to employees upon vesting of restricted stock units, net of minimum tax withholdings		1	(882)					(881)
Issuance of common shares under the employee stock purchase plan	121
Issuance of common shares under the employee stock purchase plan		1	1,541					1,542
Stock-based compensation expense			32,939					32,939
Tax benefit related to exercise of stock options			1,608					1,608
Net income				(2,176,237)				(2,176,237)
Translation adjustments					1,666			1,666
Adjustment to minimum pension liability, net					417			417
Ending Balance at Sep. 26, 2009	257,938					214
Ending Balance at Sep. 26, 2009		$2,579	$4,898,422	($2,393,881)	$7,028		($1,433)	$2,512,715

Statement Of Cash Flows Indirec

Statement Of Cash Flows Indirect (USD $)
In Thousands	12 Months Ended Sep. 26, 2009	12 Months Ended Sep. 27, 2008	12 Months Ended Sep. 29, 2007
Operating activities
Net (loss) income	($2,176,237)	($385,617)	$94,578
Adjustments to reconcile net (loss) income to net cash provided by operating activities:
Depreciation	67,195	52,413	14,291
Amortization	206,729	120,537	16,871
Fair value write-up of Cytyc and Third Wave inventory sold	1,167	46,258	0
Non-cash interest expense	17,742	20,541	181
Goodwill impairment charge	2,340,023	0	0
Acquired in-process research and development	0	565,200	0
Impairment charges of intangibles	4,065	2,900	0
Stock-based compensation expense	32,939	25,664	6,104
Excess tax benefit related to exercise of non-qualified stock options	(2,978)	(62,740)	(21,926)
Deferred income taxes	(1,941)	(10,365)	5,873
Impairment of cost-method investments	2,243	0	0
Loss on disposal and impairment of property and equipment	4,399	1,740	734
Other non-cash activity	(1,660)	2,510	(368)
Changes in operating assets and liabilities, excluding the effect of acquisitions:
Accounts receivable	57,581	(58,801)	(45,367)
Inventories	(15,142)	(29,595)	(7,997)
Prepaid income taxes	17,925	74,408	0
Prepaid expenses and other assets	(3,831)	(5,692)	269
Accounts payable	(12,881)	(10,189)	14,265
Accrued expenses and other liabilities	(10,613)	(14,596)	59,758
Deferred revenue	19,640	27,022	16,661
Net cash provided by operating activities	546,365	361,598	153,927
Investing activities
Acquisition of businesses, net of cash acquired	0	(2,584,947)	(9,793)
Payment of additional acquisition consideration	(229)	(24,394)	(19,033)
Purchase of property and equipment	(31,357)	(53,536)	(22,840)
Increase in equipment under customer usage agreements	(22,786)	(24,731)	0
Purchase of licensed technology and other intangible assets	(6,238)	0	0
Proceeds from sale of intellectual property	2,250	3,000	0
Proceeds from sale of building	0	0	1,427
Purchase of insurance contracts	(5,322)	(3,322)	(3,322)
Proceeds from sale of cost method investment	0	936	2,150
Purchase of cost method investment	(550)	0	(1,000)
Purchases of investment securities	0	(263)	0
Proceeds from sales and maturities of investment securities	0	2,638	0
Acquisition of non-controlling interest	0	0	(1,100)
Deferred acquisition costs	0	0	(6,393)
Decrease (increase) in restricted cash	2,713	(1,332)	0
Deferred gain	0	9,500	0
Net cash used in investing activities	(61,519)	(2,676,451)	(59,904)
Financing activities
Proceeds from issuance of convertible notes, net of issuance costs	0	1,688,974	0
Payments upon conversion of Cytyc convertible notes	(298)	(40,574)	0
Proceeds under credit agreements, net of issuance costs	0	2,855,609	0
Repayments under credit agreements	(290,833)	(2,425,000)	(55,000)
Proceeds from note payable	0	2,062	6,889
Repayments of notes payable	(10,127)	(2,895)	(5,884)
Excess tax benefit related to exercise of non-qualified stock options	2,978	62,740	21,926
Net proceeds from issuance of common stock pursuant to employee stock plans	10,887	171,014	10,578
Financing costs on credit agreement	(350)	0	0
Payments of employee restricted stock tax withholdings	(881)	(851)	0
Purchase of treasury shares to settle minimum withholding taxes	0	0	(969)
Net cash (used in) provided by financing activities	(288,624)	2,311,079	(22,460)
Effect of exchange rate changes on cash and cash equivalents	1,303	(968)	(1,083)
Net increase (decrease) in cash and cash equivalents	197,525	(4,742)	70,480
Cash and cash equivalents, beginning of year	95,661	100,403	29,923
Cash and cash equivalents, end of year	$293,186	$95,661	$100,403

1.Operations

1.Operations
	12 Months Ended Sep. 26, 2009 USD / shares
Notes to Financial Statements [Abstract]
1.Operations	1. Operations Hologic, Inc. (the Company or Hologic) develops, manufactures and distributes medical imaging systems and diagnostic and surgical products focused on the healthcare needs of women. In October 2007 (the first quarter of fiscal 2008), the Company completed its merger with Cytyc Corporation (Cytyc), a company that develops, manufactures and markets complementary products covering a range of cancer and womens health applications, including cervical cancer screening, treatment of excessive menstrual bleeding and radiation treatment of early-stage breast cancer. As a result of the Companys merger with Cytyc, as more fully described in Note 3, the Company has become one of the largest companies in the world focused on womens health.

2.Summary of Significant Accoun

2.Summary of Significant Accounting Policies
	12 Months Ended Sep. 26, 2009 USD / shares
Notes to Financial Statements [Abstract]
2.Summary of Significant Accounting Policies	2. Summary of Significant Accounting Policies Principles of Consolidation The consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries. All intercompany transactions and balances have been eliminated in consolidation. The Companys fiscal year ends on the last Saturday in September. Fiscal 2009, 2008 and 2007 ended on September26, 2009, September27, 2008, and September29, 2007, respectively, and each fiscal year presented included 52 weeks. Reclassifications The Company reclassified other receivable amounts of $5,902 from Accounts receivable to Prepaid expenses and other current assets for fiscal 2008 to conform to the current period presentation. The Company also reclassified certain amounts in the Consolidated Statement of Cash Flows for fiscal 2008 and 2007 to conform to the current period presentation. As a result, net cash provided by operations decreased to $361,598 from $364,596 for fiscal 2008 primarily due to reclassifying changes in certain other assets and other liabilities to cash flows provided by operating activities from investing activities aggregating $3,849 offset by reclassifying $851 of payments to tax authorities for tax withholdings on the vesting of restricted stock units issued to employees as a cash outflow in the financing section. As result of these changes cash used in investing activities for fiscal 2008 decreased to $2,676,451 from $2,680,300 and cash provided by financing activities decreased to $2,311,079 from $2,311,930. In addition, there were insignificant reclassifications of certain amounts within the line items of the investing activities section. For fiscal 2007, the Company reclassified changes in certain other assets and other liabilities to cash flows provided by operating activities from investing activities resulting in cash flows from operations increasing to $153,927 from $153,250 and cash used in investing activities increasing to $59,904 from $59,226. Subsequent Events Consideration The Company considers events or transactions that occur after the balance sheet date but prior to the issuance of the financial statements to provide additional evidence relative to certain estimates or to identify matters that require additional disclosure. Subsequent events have been evaluated through November24, 2009, the date these financial statements are considered issued, and the financial statements reflect those material items that arose after the balance sheet date but prior to this date that would be considered recognized subsequent events. Subsequent to September26, 2009, the Company made voluntary payments of $21,000 on its term notes, and as such, the Company reclassified this amount to short-term debt from long-term debt, which is reflected in the Consolidated Balance Sheet. There were no other material recognized subsequent events recorded in the September26, 2009 consolidated financial statements. Stock Split On April2, 2008, the Company effected a two-for-one stock split in the form of a stock dividend. The stock split is retroactively reflected in the accompanying consolidated financial statements and notes for all per

3.Business Combinations

3.Business Combinations
	12 Months Ended Sep. 26, 2009 USD / shares
Notes to Financial Statements [Abstract]
3.Business Combinations	3. Business Combinations Fiscal 2008 Acquisitions: Acquisition of Third Wave Technologies, Inc. On July24, 2008,the Company completed its acquisition of Third Wave Technologies, Inc. (Third Wave) pursuant to a definitive agreement dated June8, 2008. The Company concluded that the acquisition of Third Wave did not represent a material business combination and therefore no pro forma financial information has been provided herein. Subsequent to the acquisition date, the Companys results of operations include the results of Third Wave, which is a component of the Companys Diagnostics reporting segment. Third Wave, located in Madison, Wisconsin, develops and markets molecular diagnostic reagents for a wide variety of DNA and RNA analysis applications based on its proprietary Invader chemistry. Third Waves current clinical diagnostic offerings consist of products for conditions such as Cystic Fibrosis, cardiovascular risk and other diseases. In March 2009, Third Wave received approval from the U.S. Food and Drug Administration (FDA) for two human papillomavirus (HPV) tests; Cervista HPV High Risk (HR) and Cervista HPV 16/18. The Company paid $11.25 per share of Third Wave, for an aggregate purchase price of approximately $591,100 (subject to adjustment) consisting of approximately $575,400 in cash in exchange for stock and warrants; approximately 668 of fully vested stock options granted to Third Wave employees in exchange for their vested Third Wave stock options, with an estimated fair value of approximately $8,100; and approximately $7,600 for acquisition related fees and expenses. There are no potential contingent consideration arrangements payable to the former shareholders in connection with this transaction. Additionally, the Company granted approximately 315 unvested stock options in exchange for unvested Third Wave stock options, with an estimated fair value of approximately $5,100, which is being recognized as compensation expense over the vesting period. The Company determined the fair value of the options issued in connection with the acquisition in accordance with EITF Issue No.99-12, Determination of the Measurement Date for the Market Price of Acquirer Securities Issued in a Purchase Business Combination). The Company determined the measurement date to be July24, 2008, the date the transaction was completed, as the number of shares to be issued according to the exchange ratio was not fixed until this date. The Company valued the securities based on the average market price for two days before the measurement date and the measurement date itself. The weighted average stock price was determined to be $23.54. The purchase price is as follows: Cash portion of consideration $ 575,400 Fair value of vested options exchanged 8,100 Direct acquisition costs 7,600 Total purchase price $ 591,100 The fair value of vested Hologic common stock options exchanged for vested Third Wave options was included in the purchase price as such options were fully vested. The Company estimated the fair value of these stock options using the Binomial Option Pricing Model a

4.Sale of Gestiva

4.Sale of Gestiva
	12 Months Ended Sep. 26, 2009 USD / shares
Notes to Financial Statements [Abstract]
4.Sale of Gestiva	4. Sale of Gestiva On January16, 2008, the Company entered into a definitive agreement pursuant to which it agreed to sell full U.S. and world-wide rights to Gestiva to K-V Pharmaceutical Company upon approval of the pending Gestiva new drug application (the Gestiva NDA) by the FDA for a purchase price of $82,000. The Company received $9,500 of the purchase price in fiscal 2008, and the balance is due upon final approval of the Gestiva NDA by the FDA on or before February19, 2010 and the production of a quantity of Gestiva suitable to enable the commercial launch of the product. Either party has the right to terminate the agreement if FDA approval is not obtained by February 19, 2010. The Company agreed to continue its efforts to obtain FDA approval of the NDA for Gestiva as part of this arrangement. All costs incurred in these efforts will be reimbursed by K-V Pharmaceutical and are being recorded as a credit against research and development expenses. During fiscal 2009 and 2008, these reimbursed costs were not material. The Company recorded the $9,500 as a deferred gain within current liabilities in the Consolidated Balance Sheet. The Company expects that the gain will be recognized upon the closing of the transaction following final FDA approval of the Gestiva NDA or if the agreement is terminated. The Company cannot assure that it will be able to obtain the requisite FDA approval, that the transaction will be completed or that it will receive the balance of the purchase price.Moreover, if K-V Pharmaceutical terminates the agreement as a result of a breach by the Company of a material representation, warranty, covenant or agreement, the Company will be required to return the funds previously received as well as expenses reimbursed by K-V. The development of Gestiva, a drug that, if approved by the FDA, could be used in the prevention of preterm birth in pregnant women with a history of at least one spontaneous preterm birth, was originally begun by Adeza Biomedical Corporation, which was acquired by Cytyc on April2, 2007. On October22, 2007, the Company completed its merger with Cytyc and as a result acquired all rights to Gestiva. The Company allocated $53,400 to acquired in-process research and development as part of the initial purchase price allocation.

5.Borrowings and Credit Arrange

5.Borrowings and Credit Arrangements
	12 Months Ended Sep. 26, 2009 USD / shares
Notes to Financial Statements [Abstract]
5.Borrowings and Credit Arrangements	5. Borrowings and Credit Arrangements The Company had total debt of $1,903,328 at September26, 2009 and $2,200,900 at September27, 2008. The Companys borrowings consisted of the following at September26, 2009 and September27, 2008: 2009 2008 Current debt obligations: Term Loan A $ 28,789 $ 34,444 Term Loan B 6,785 1,723 AEG debt 1,500 2,015 Cytyc notes 298 Other 1,299 Total current debt obligations 38,373 38,480 Long-term debt obligations: Term Loan A 95,929 310,000 Term Loan B 42,664 118,833 AEG debt 8,587 Other 1,362 139,955 437,420 Convertible notes 1,725,000 1,725,000 Total long-term debt obligations 1,864,955 2,162,420 Total debt obligations $ 1,903,328 $ 2,200,900 As of September26, 2009, the debt maturity schedule for the Companys term loans as well as other components of its debt obligations is as follows for each fiscal year: 2010 2011 2012 2013 2014 Total Term Loan A $ 28,789 $ 18,227 $ 18,227 $ 59,475 $ $ 124,718 Term Loan B 6,785 628 628 41,408 49,449 AEG debt 1,500 1,500 Other 1,299 1,362 2,661 Convertible Notes (1) 1,725,000 1,725,000 $ 38,373 $ 20,217 $ 18,855 $ 100,883 $ 1,725,000 $ 1,903,328 (1) The earliest date of redemption is December13, 2013, which is in fiscal 2014 Credit Agreement On October22, 2007, the Company and certain of its domestic subsidiaries entered into a senior secured credit agreement (the Credit Agreement) with Goldman Sachs Credit Partners L.P. and certain other lenders, (collectively, the Lenders). Pursuant to the terms and conditions of the Credit Agreement, the Lenders committed to provide senior secured financing in an aggregate amount of up to $2,550,000. As of the closing of the merger with Cytyc, the Company borrowed $2,350,000 under the credit facilities. The Company used the proceeds from the credit facilities to pay the cash consideration of the merger with Cytyc, and to pay fees, commissions and expenses incurred by the Company in connection with the merger with Cytyc and the Credit Agreement. In addition, the Company used the proceeds of the credit facilities, together with the Companys available cash, to pay the cash due upon conversion of Cytycs 2.25% Senior Convertible Notes due 2024 that were outstanding after the closing of the merger with Cytyc. The credit facilities under the Credit Agreement consisted of: $600,000 senior secured Term Loan A (the Term Loan A facility) with a final maturity date of September30, 2012; $250,000 senior secured Term Loan B-1 and $250,000 senior secured Term Loan B-2 (collectively, the Term Loan B facility) with a final maturity date of March31

6.Fair Value Measurements

6.Fair Value Measurements
	12 Months Ended Sep. 26, 2009 USD / shares
Notes to Financial Statements [Abstract]
6.Fair Value Measurements	6. Fair Value Measurements Effective September28, 2008, the Company adopted ASC 820, Fair Value Measurements and Disclosures (formerly SFAS No.157, Fair Value Measurement ), for its financial assets and financial liabilities that are re-measured and reported at fair value at each reporting period and its nonfinancial assets and nonfinancial liabilities that are re-measured and reported at fair value at least annually. As permitted, the Company has elected to defer implementation of ASC 820 as it relates to its nonfinancial assets and nonfinancial liabilities that are recognized and disclosed at fair value in the financial statements on a non-recurring basis until September27, 2009. The Company is evaluating the impact, if any, ASC 820 will have on its nonfinancial assets and nonfinancial liabilities. The adoption of ASC 820 for financial assets and financial liabilities that are re-measured and reported at fair value on a recurring basis did not have an impact on the Companys financial results. ASC 820 establishes a three-level valuation hierarchy for disclosure of fair value measurements. Financial assets and financial liabilities are categorized within the valuation hierarchy based upon the lowest level of input that is significant to the measurement of fair value. The three levels of the hierarchy are defined as follows: Level 1Inputs to the valuation methodology are quoted market prices for identical assets or liabilities. Level 2Inputs to the valuation methodology are other observable inputs, including quoted market prices for similar assets or liabilities and market-corroborated inputs. Level 3Inputs to the valuation methodology are unobservable inputs based on managements best estimate of inputs market participants would use in pricing the asset or liability at the measurement date, including assumptions about risk. As of September26, 2009, the Companys financial assets that are re-measured at fair value on a recurring basis consisted of $313 in money market mutual funds that are classified as cash and cash equivalents in the Consolidated Balance Sheets. As there are no withdrawal restrictions, they are classified within Level1 of the fair value hierarchy and are valued using quoted market prices for identical assets. The Company holds certain minority cost-method equity investments in non-publicly traded securities aggregating $7,585 and $9,278 at September26, 2009 and September27, 2008, respectively, which are included in other long-term assets on the Companys Consolidated Balance Sheets. These investments are generally carried at cost. As the inputs utilized for the Companys periodic impairment assessment are not based on observable market data, these cost method investments are classified within Level 3 of the fair value hierarchy on a non-recurring basis. To determine the fair value of these investments, the Company uses all available financial information related to the entities, including information based on recent or pending third-party equity investments in these entities. In certain instances, a cost method investments fair value is not estimated as there are no

7.Pension and Other Employee Be

7.Pension and Other Employee Benefits
	12 Months Ended Sep. 26, 2009 USD / shares
Notes to Financial Statements [Abstract]
7.Pension and Other Employee Benefits	7. Pension and Other Employee Benefits The Company has certain defined benefit pension plans covering the employees of its AEG German subsidiary (the Pension Benefits). As of September29, 2007, the Company adopted SFAS No.158, Employers Accounting for Defined Benefit Pension and Other Postretirement Plans, an amendment of FASB Statements No.87, 88, 106 and 132(R) (codified primarily in ASC 715, Defined Benefit Plans) using a prospective approach. The adoption of this Standard did not impact the Companys compliance with its debt covenants under its credit agreements, cash position or results of operations. The following table summarizes the incremental effect of adopting this Standard on individual line items in the Consolidated Balance Sheet as of September29, 2007: Before Adoption of SFASNo.158 Adjustments (Inthousands) After Adoption of SFASNo.158 Accumulated other comprehensive income $ $ 2,212 $ 2,212 Total stockholders equity $ 803,511 $ 2,212 $ 805,723 As of September26, 2009 and September27, 2008, the Companys pension liability is $6,736 and $7,323, respectively, which is primarily recorded as a component of long-term liabilities in the Consolidated Balance Sheets. Under German law, there are no rules governing investment or statutory supervision of the pension plan. As such, there is no minimum funding requirement imposed on employers. Pension benefits are safeguarded by the Pension Guaranty Fund, a form of compulsory reinsurance that guarantees an employee will receive vested pension benefits in the event of insolvency. The tables below provide a reconciliation of benefit obligations, plan assets, funded status, and related actuarial assumptions of the Companys German Pension Benefits. Change in Benefit Obligation PensionBenefits September26, 2009 September27, 2008 September29, 2007 Benefit obligation at beginning of year $ (7,323 ) $ (7,627 ) $ (8,005 ) Service cost Interest cost (469 ) (424 ) (397 ) Plan participants contributions Actuarial gain 764 665 1,455 Foreign exchange (28 ) (229 ) (947 ) Benefits paid 320 292 267 Benefit obligation at end of year (6,736 ) (7,323 ) (7,627 ) Plan assets Funded status $ (6,736 ) $ (7,323 ) $ (7,627 ) The tables below outline the components of the net periodic benefit cost and related actuarial assumptions of the Companys German Pension Benefits plan. Components of Net Periodic Benefit Cost PensionBenefits 2009 2008 2007 Service cost $ $ $ Interest cost 469 424 397 Expected return on plan assets Amortization of prior service cost Recognized net actuarial gain (169 ) (93 ) (91 ) Net periodic benefit cost $ 300 $ 331 $ 306

8.Income Taxes

8.Income Taxes
	12 Months Ended Sep. 26, 2009 USD / shares
Notes to Financial Statements [Abstract]
8.Income Taxes	8. Income Taxes The Company accounts for income taxes using the liability method as required by ASC 740, Income Taxes (formerly SFAS No.109, Accounting for Income Taxes). Under this method, deferred income taxes are recognized for the future tax consequences of differences between the tax and financial accounting bases of assets and liabilities at the end of each reporting period. Deferred income taxes are based on enacted tax laws and statutory tax rates applicable to the periods in which the differences are expected to affect taxable income. A valuation allowance is established when necessary to reduce deferred tax assets to the amounts expected to be realized. The provision for income taxes consisted of the following: Years ended September26, 2009 September27, 2008 September29, 2007 Federal: Current $ 74,311 $ 102,212 $ 39,096 Deferred 4,447 (10,835 ) 6,053 78,758 91,377 45,149 State: Current 9,804 10,411 6,735 Deferred (6,210 ) 265 (2,101 ) 3,594 10,676 4,634 Foreign: Current 5,388 4,218 6,167 Deferred (178 ) 205 (2,039 ) 5,210 4,423 4,128 $ 87,562 $ 106,476 $ 53,911 A reconciliation of income taxes at the U.S. federal statutory rate to the Companys effective tax rate is as follows: Years ended September26, 2009 September27, 2008 September29, 2007 Income tax provision at federal statutory rate (35.0 )% (35.0 )% 35.0 % Increase (decrease) in tax resulting from: Goodwill impairment 39.1 Section199 manufacturing deduction (0.3 ) (2.2 ) State income taxes, net of federal benefit 0.3 2.5 3.3 In-process research and development 71.2 State law change (0.1 ) 0.8 Tax credits (0.2 ) (0.6 ) (1.4 ) Permanent differences 0.2 1.0 (0.7 ) Change in valuation allowance 0.1 (0.4 ) Other 0.1 0 .4 0.5 4.2 % 38.1 % 36.3 % The Companys (loss) income before income taxes consisted of the following: Years ended September26, 2009 September27, 2008 September29, 2007 Domestic $ (2,095,809 ) $ (275,091 ) $ 137,659 Foreign 7,134 (4,050 ) 10,830 $ (2,088,675 ) $ (279,141 ) $ 148,489 Significant components of the Companys deferred tax assets and liabilities are as follows: September26, 2009 September27, 2008 Deferred tax assets Net operating loss carryforwards $ 96,170 $ 123,377 Nondeductible accruals 18,533 19,038 Nondeductible reserves 9,773 7,068 Stock-ba

9.Stockholders' Equity and Stoc

9.Stockholders' Equity and Stock-Based Compensation
	9/28/2008 - 9/26/2009 USD / shares
Notes to Financial Statements [Abstract]
9.Stockholders' Equity and Stock-Based Compensation	9. Stockholders Equity and Stock-Based Compensation Common Shares Authorization On October22, 2007, the Companys certificate of incorporation was amended to increase the number of authorized shares of the Companys common stock thereunder from 180,000 to 600,000. At the Companys March11, 2008 Annual Meeting of Stockholders, an increase in the number of authorized shares of common stock from 600,000 to 750,000 was approved. Rights Agreement On April2, 2008, the Company entered into an Amended and Restated Rights Agreement (the Amended and Restated Rights Agreement) between the Company and American Stock Transfer Trust Company as Rights Agent (the Rights Agent). The Amended and Restated Rights Agreement amends and restates the Companys rights agreement, dated as of September17, 2002, as amended on May21, 2007, between the Company and the Rights Agent. On April2, 2008, the Company effected a two-for-one stock split in the form of a stock dividend to stockholders as of March21, 2008. Pursuant to the Amended and Restated Rights Agreement, the Company amended the terms of the rights issued and issuable under the agreement (Rights), effective as of April3, 2008 (after the stock dividend), to reset the Rights such that each share of Common Stock is entitled to receive one Right, to retain the purchase price of each Right at $60 per Right, and to provide that each Right will entitle the holder to purchase one twenty-five thousandth of a share of Series A Junior Participating Preferred Stock (the Series A Preferred Stock). Conforming changes have also been made to the Companys certificate of designation for the Series A Preferred Stock to provide that each share of Series A Preferred Stock carries 25,000 times the dividend, liquidation and voting rights of the Companys Common Stock. Other modifications have also been made in the Amended and Restated Rights Agreement to update the agreement for certain developments, including the recent amendments to the Companys by-laws permitting stockholders to hold and transfer shares of the Companys capital stock in book entry form. The expiration date of the Rights has remained unchanged at January1, 2013. Stock-Based Compensation Equity Compensation Plans The Company has one share-based compensation plan pursuant to which awards are currently being madethe 2008 Equity Incentive Plan. The Company has four share-based compensation plans pursuant to which outstanding awards have been made, but from which no further awards can or will be madei) the 1995 Combination Stock Option Plan; ii) the 1997 Employee Equity Incentive Plan; iii) the 1999 Equity Incentive Plan; and iv) the 2000 Acquisition Equity Incentive Plan. At the Companys March11, 2008 Annual Meeting of Stockholders, the Companys 2008 Equity Incentive Plan (the 2008 Equity Plan) was approved. In connection with this approval, the Companys 1999 Second Amended and Restated Equity Incentive Plan was terminated. The purpose of the 2008 Equity Plan is to provide stock options, stock issuances and other equity interests in the Company to employees, officers, directors, consultants and advisors of the Company and its parents an

10.Profit Sharing 401

10.Profit Sharing 401(k) Plan
	12 Months Ended Sep. 26, 2009 USD / shares
Notes to Financial Statements [Abstract]
10.Profit Sharing 401(k) Plan	10. Profit Sharing 401(k) Plan The Company has a qualified profit sharing plan covering substantially all of its employees. Contributions to the plan are at the discretion of the Companys Board of Directors. The Company made contributions of $5,725, $5,305 and $1,572 for fiscal years 2009, 2008 and 2007, respectively.

11.Supplemental Executive Retir

11.Supplemental Executive Retirement Plan
	12 Months Ended Sep. 26, 2009 USD / shares
Notes to Financial Statements [Abstract]
11.Supplemental Executive Retirement Plan	11. Supplemental Executive Retirement Plan Effective March15, 2006, the Company adopted a SERP to provide non-qualified retirement benefits to a select group of executive officers, senior management and highly compensated employees of the Company. Eligible employees may elect to contribute up to 75% of their annual base salary and 100% of their annual bonus to the SERP and such employee contributions are 100% vested. In addition, the Company may elect to make annual discretionary contributions on behalf of participants in the SERP. Each Company contribution is subject to a three year vesting schedule, such that each contribution vests one third annually. Employee contributions are recorded within accrued expenses in the Consolidated Balance Sheets. Upon enrollment into the SERP, employees make investment elections for both their voluntary contributions and discretionary contributions, if any, made by the Company. Earnings and losses on contributions based on these investment elections are recorded as a component of compensation expense in the period earned. On October30, 2006 and October22, 2007, the Compensation Committee of the Board of Directors approved a $1,500 discretionary cash contribution to the SERP for each year. In November 2008, the Compensation Committee of the Board of Directors approved a $2,825 discretionary contribution to the SERP for fiscal 2008. Discretionary contributions by the Company to the SERP are held in a Rabbi Trust. The Company is recording compensation expense for the SERP discretionary contribution ratably over the three-year vesting period, which totaled $1,815, $876 and $442 in fiscal years 2009, 2008 and 2007, respectively. The full amount of the discretionary contribution, net of forfeitures, is recorded within accrued expenses in the Consolidated Balance Sheets. The Company has purchased Company-owned group life insurance contracts, in which both voluntary and discretionary Company SERP contributions are invested, to fund payment of the Companys obligation to the SERP participants. The total amount invested at September26, 2009 and September27, 2008 was $11,602 and $5,575, respectively, which approximated the total of employee voluntary contributions into the plan and the Companys cash portion of its discretionary contribution. The values of these life insurance contracts are recorded with other long-term assets in the Consolidated Balance Sheets. Changes in the cash surrender value of life insurance contracts, which were immaterial in fiscal 2009, 2008 and 2007, are recorded as a component of (expense) other income, net in the Consolidated Statement of Operations.

12.Commitments and Contingencie

12.Commitments and Contingencies
	12 Months Ended Sep. 26, 2009 USD / shares
Notes to Financial Statements [Abstract]
12.Commitments and Contingencies	12. Commitments and Contingencies Contingent Earn-Out Payments As a result of the merger with Cytyc, the Company assumed the obligation to the former Adiana stockholders to make contingent earn-out payments tied to the achievement of milestones. The milestone payments include potential contingent payments of up to $155,000 based on worldwide sales of the Adiana Permanent Contraception System in the first year following FDA approval and on annual incremental sales growth thereafter through December31, 2012. FDA approval of the Adiana Permanent Contraception System occurred on July6, 2009, and the Company began accruing contingent consideration in the fourth quarter of fiscal 2009 based on the defined percentage of worldwide sales of the product. The total accrued contingent consideration, net at September26, 2009 is $1,454. These amounts are being recorded as additional purchase price, and under the terms of the agreement the first payment is not due to the Adiana shareholders until October 2010. The agreement includes an indemnification provision that provides for the reimbursement of qualifying legal expenses in defense of the Adiana intellectual property, and the Company has the right to offset contingent consideration payments to the Adiana shareholders with these qualifying legal costs (see Note 15). Legal costs have not been material to date. The Company satisfied its obligation for a second and final earn-out to the former Suros Surgical stockholders related to Suros incremental revenue growth for revenues earned through July31, 2008. The Company accrued an amount of approximately $24,500 for this second annual earn-out in the fourth quarter of 2008, with an increase to goodwill, of which $24,400 was paid as of September27, 2008 and the remainder was paid as of December27, 2008. The Company had also made a payment of approximately $19,000 to the former Suros stockholders in the fourth quarter of fiscal 2007 for the first year earn-out. Finance Lease Obligations As a result of the merger with Cytyc, the Company assumed the obligation to a non-cancelable lease agreement for a building with approximately 164,000 square feet located in Alajuela, Costa Rica, to be used as a manufacturing and office facility to replace its existing Costa Rica facility. The Company moved into this new location during fiscal 2009. The Company was responsible for a significant portion of the construction costs and therefore was deemed, for accounting purposes, to be the owner of the building during the construction period, in accordance with ASC 840, Leases, Subsection 40-15-5. During the year ended September27, 2008, the Company recorded an additional $4,400 in fair market value of the building, which was completed in fiscal 2008. This is in addition to the $3,000 fair market value of the land and the $7,700 fair market value related to the building constructed that Cytyc had recorded as of October22, 2007. The Company has recorded such fair market value within property and equipment on its Consolidated Balance Sheets. At September26, 2009, the Company has recorded $1,508 in accrued expenses and $16,329 in other long-term liabilities re

13.Business Segments and Geogra

13.Business Segments and Geographic Information
	12 Months Ended Sep. 26, 2009 USD / shares
Notes to Financial Statements [Abstract]
13.Business Segments and Geographic Information	13. Business Segments and Geographic Information The Company reports segment information in accordance with ASC 280, Segment Reporting (formerly SFAS No.131, Disclosures about Segments of an Enterprise and Related Information). Operating segments are identified as components of an enterprise about which separate, discrete financial information is available for evaluation by the chief operating decision maker, or decision-making group, in making decisions how to allocate resources and assess performance. The Companys chief operating decision maker is the president, and the Companys reportable segments have been identified based on the end markets to which its product are sold into. Each reportable segment generates revenue from either the sale of medical equipment and related services and/or sale of disposable supplies, primarily used in providing diagnostic tests and surgical procedures. As of September26, 2009, the Company has four reportable segments. Certain reportable segments represent an aggregation of operating units within each segment. The Company measures and evaluates its reportable segments based on segment revenues and operating income (loss). In fiscal 2008, as a result of the merger with Cytyc, the Company reassessed its segment reporting based on the operating and reporting structure of the combined company. Beginning in fiscal 2008, the Company combined its previously reported Other Business segment with its Breast Health (formerly Mammography/Breast Care) and Skeletal Health (formerly Osteoporosis) segments, to better reflect how the Company views its operations and manages its business. The Companys Other Business segment previously included AEG, mini C-arm, extremity MRI, conventional general radiography service and digital general radiography systems businesses. The AEG business is now part of Breast Health while the remaining reporting units are part of Skeletal Health. In addition, the Company began reporting two new operating segments: Diagnostics and GYN Surgical. Diagnostics includes the ThinPrep Products and the Rapid Fetal Fibronectin test, as well as the Companys proprietary Invader chemistry and two Cervista HPV tests obtained in the Third Wave acquisition, which received FDA approval in fiscal 2009. GYN Surgical includes the NovaSure system and the Adiana Permanent Contraception System, which received FDA approval in fiscal 2009. The MammoSite Radiation Therapy system, previously part of Cytycs surgical reporting segment, which is a single-use device for the treatment of early-stage breast cancer, is part of the Companys Breast Health segment. The Company received FDA approval for its multi-lumen product, MammoSite ML, in August 2009.The Diagnostic segment also includes the results of Third Wave, which was acquired in the fourth quarter of fiscal 2008. As a result of these changes in fiscal 2008, the Company reports its business as four segments: Breast Health, Diagnostics, GYN Surgical and Skeletal Health. Identifiable assets for the four principal operating segments consist of inventories, intangible assets, and property and equipment. The Company fully allocates depreciation expense to its

14.Accrued Expenses and Other L

14.Accrued Expenses and Other Long-Term Liabilities
	12 Months Ended Sep. 26, 2009 USD / shares
Notes to Financial Statements [Abstract]
14.Accrued Expenses and Other Long-Term Liabilities	14. Accrued Expenses and Other Long-Term Liabilities Accrued expenses and other long-term liabilities consist of the following: September26, 2009 September27, 2008 Accrued Expenses Accrued compensation and employee benefits $ 51,727 $ 68,204 Accrued commissions 14,325 15,768 Accrued income and other taxes 18,056 11,744 Accrued interest 10,184 11,284 Accrued warranty, current portion 5,602 9,080 Other accrued expenses 37,390 38,666 $ 137,284 $ 154,746 September26, 2009 September27, 2008 OtherLong-Term Liabilities Accrued lease obligationlong-term $ 31,650 $ 31,164 Reserve for income tax uncertainties 14,728 12,307 Pension liabilitieslong-term 6,404 6,995 Other 5,752 6,987 $ 58,534 $ 57,453

15.Litigation and Other Matters

15.Litigation and Other Matters
	12 Months Ended Sep. 26, 2009 USD / shares
Notes to Financial Statements [Abstract]
15.Litigation and Other Matters	15. Litigation and Other Matters On October5, 2007, Ethicon Endo-Surgery, Inc., a Johnson Johnson operating company, filed a complaint against the Company and its wholly-owned subsidiary Suros in the United States District Court for the Southern District of Ohio, Western Division. The complaint alleges that certain of the ATEC biopsy systems manufactured and sold by Suros infringe four Ethicon patents. An amended complaint filed January11, 2008 additionally asserts claims of unfair competition. The complaint seeks to enjoin Hologic and Suros from conducting acts of unfair competition and infringing the patents as well as the recovery of unspecified damages and costs. A Markman hearing was held on January8, 2009, and the Court issued its ruling on April3, 2009. A court ordered settlement conference occurred on August11, 2009 without any resolution. This suit is currently scheduled to go to trial on February1, 2010. The Company is unable to reasonably estimate the ultimate outcome of this case. On May22, 2009, Conceptus, Inc. filed suit in the United States District Court for the Northern District of California seeking a declaration by the Court that Hologics planned importation, use, sale or offer to sell of its forthcoming Adiana Permanent Contraception System, would infringe five Conceptus patents. On July9, 2009, Conceptus filed an amended complaint alleging infringement of the same five patents by the Adiana Permanent Contraception System. The complaint seeks preliminary and permanent injunctive relief and unspecified monetary damages. In addition to the amended complaint, Conceptus also filed a motion for preliminary injunction seeking to preliminarily enjoin sales of the Adiana System based on alleged infringement of certain claims of three of the five patents. A hearing on Conceptus preliminary injunction motion was held on November4, 2009, and on November6, 2009, the judge issues an order denying the motion. A hearing on claim construction is scheduled for March10, 2010. A trial date has not been set. Based on the early stage of this litigation, the Company is unable to reasonably estimate the ultimate outcome of this case. On August6, 2009, Ethicon Endo-Surgery, Inc., a Johnson Johnson operating company, filed a complaint against the Company and its wholly-owned subsidiary Suros in the United States District Court for the District of Delaware. The complaint alleges that certain of the Eviva biopsy systems manufactured and sold by Suros infringe four Ethicon patents. The complaint seeks to enjoin Hologic and Suros from infringing the patents as well as recovery of damages and costs resulting from the alleged infringement. Based on the early stage of this litigation, the Company is unable to reasonably estimate the ultimate outcome of this case. As of September26, 2009, the Company does not believe a loss is probable in any of the matters disclosed above. The Company is a party to various other legal proceedings and claims arising out of the ordinary course of its business. The Company believes that except for those described above there are no other proceedings or claims pending against it the ultimate resolution

16.Quarterly Statement of Opera

16.Quarterly Statement of Operations Information (Unaudited)
	12 Months Ended Sep. 26, 2009 USD / shares
Notes to Financial Statements [Abstract]
16.Quarterly Statement of Operations Information (Unaudited)	16. Quarterly Statement of Operations Information (Unaudited) The following table presents a summary of quarterly results of operations for fiscal 2009 and 2008: 2009 First Quarter Second Quarter Third Quarter Fourth Quarter Total revenue $ 429,233 $ 402,014 $ 403,120 $ 402,767 Gross profit (1) 229,959 209,574 211,145 206,808 Net income (loss) (2) 47,993 (2,300,170 ) 41,000 34,940 Diluted net income (loss) per common share $ 0.19 $ (8.97 ) $ 0.16 $ 0.13 2008 First Quarter Second Quarter Third Quarter Fourth Quarter Total revenue (3) $ 371,445 $ 431,048 $ 429,492 $ 442,513 Gross profit 167,835 239,638 244,763 240,281 Net income (loss) (2) (358,608 ) 55,986 61,379 (144,374 ) Diluted net income(loss) per common share $ (1.65 ) $ 0.22 $ 0.24 $ (0.56 ) (1) During the third quarter of fiscal 2009, the Company determined that certain amounts previously classified as a component of selling and marketing expenses should be reclassified to cost of product sales. As a result, gross profit was reduced by $704 in the first quarter and $689 in the second quarter of fiscal 2009. (2) See Note 2 for further discussion of goodwill impairment charges recorded in the second quarter of fiscal 2009, and see Note 3 for further discussion of in-process research and development expenses incurred in the first and fourth quarters of fiscal 2008 related to the merger with Cytyc and Third Wave acquisition. (3) The sum of the quarterly total revenue does not agree with the Consolidated Statements of Operations due to rounding.

17.Subsequent Event

17.Subsequent Event
	12 Months Ended Sep. 26, 2009 USD / shares
Notes to Financial Statements [Abstract]
17.Subsequent Event	17. Subsequent Event On November5, 2009, the Companys Board of Directors appointed Robert Cascella, its President and Chief Operating Officer, to the position of President and Chief Executive Officer. John Cumming, our former Chairman and Chief Executive Officer, will remain with the Company as Chairman and an executive officer. In connection with this change in responsibilities, the Company made a payment of $1,750 to the Chairman and provided that he remains employed by the Company on the first and second anniversary of the effective date of the change, he will receive additional payments of $1,725 for each period.

Document Information

Document Information
	12 Months Ended Sep. 26, 2009 USD / shares
Document Information [Text Block]
Document Type	10-K
Amendment Flag	false
Document Period End Date	2009-09-26

Entity Information

Entity Information (USD $)
	12 Months Ended Sep. 26, 2009	Nov. 18, 2009	Mar. 27, 2009
Entity [Text Block]
Trading Symbol	HOLX
Entity Registrant Name	HOLOGIC INC
Entity Central Index Key	0000859737
Current Fiscal Year End Date	--09-26
Entity Well-known Seasoned Issuer	Yes
Entity Current Reporting Status	Yes
Entity Voluntary Filers	No
Entity Filer Category	Large Accelerated Filer
Entity Common Stock, Shares Outstanding		257,963,830
Entity Public Float			$3,448,132,346