UNITED STATES SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

FORM 11-K

FOR ANNUAL REPORTS OF EMPLOYEE STOCK
PURCHASE, SAVINGS AND SIMILAR PLANS
PURSUANT TO SECTION 15(d) OF THE
SECURITIES EXCHANGE ACT OF 1934

Mark One

þ		ANNUAL REPORT PURSUANT TO SECTION 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the fiscal year ended December 31, 2006

OR

o		TRANSITION REPORT PURSUANT TO SECTION 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

Commission File No.: 001-16577

     A. Full title of the plan and the address of the plan, if different from that of the issuer named below:

Flagstar Bank 401(k) Plan

     B. Name of issuer of the securities held pursuant to the plan and the address of its principal executive office:

Flagstar Bancorp, Inc.

5151 Corporate Drive

Troy, MI 48098

 

 

TABLE OF CONTENTS

Report of Independent Registered Public Accounting Firm			3
Financial Statements
Statements of Net Assets Available for Benefits			4
Statement of Changes in Net Assets Available for Benefits			5
Notes to Financial Statements			6
Supplemental Information
Schedule H, line 4i — Schedule of Assets (Held at End of Year)			11
Signatures			15
Exhibit – 23			16
Consent of Independent Registered Public Accounting Firm

REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

To the Participants and Administrator of

Flagstar Bank 401(k) Plan

We have audited the accompanying statements of net assets available for benefits of Flagstar Bank 401(k) Plan (the “Plan”) as of December 31, 2006 and 2005, and the related statement of changes in net assets available for benefits for the year ended December 31, 2006. These financial statements are the responsibility of the Plan’s management. Our responsibility is to express an opinion on these financial statements based on our audits.

We conducted our audits in accordance with the standards of the Public Company Accounting Oversight Board (United States). Those standards require that we plan and perform the audits to obtain reasonable assurance about whether the financial statements are free of material misstatement. The Plan is not required to have, nor were we engaged to perform an audit of its 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 Plan’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. An audit also includes assessing the accounting principles used and significant estimates made by management, as well as 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 net assets available for benefits of the Plan as of December 31, 2006 and 2005, and the changes in net assets available for benefits for the year ended December 31, 2006, in conformity with accounting principles generally accepted in the United States of America.

Our audits were performed for the purpose of forming an opinion on the basic financial statements taken as a whole. The supplemental schedule, Schedule H, line 4i–Schedule of Assets (Held at End of Year), is presented for the purpose of additional analysis and is not a required part of the basic 2006 financial statements, but is supplementary information required by the Department of Labor Rules and Regulations for Reporting and Disclosure under the Employee Retirement Income Security Act of 1974. This supplemental schedule is the responsibility of the Plan’s management. The supplemental schedule has been subjected to the auditing procedures applied in our audits of the basic 2006 financial statements and, in our opinion, is fairly stated in all material respects in relation to the basic financial statements taken as a whole.

/s/ Virchow, Krause & Company, LLP

Southfield, Michigan
June 22, 2007

Flagstar Bank 401(k) Plan

		December 31,
		2006				2005
Assets
Investments — at fair value
Flagstar Bancorp, Inc. common stock		$	12,889,505			$	12,381,408
Mutual funds			65,638,131				55,748,380
Money market funds			7,857,193				6,973,753
Common/Collective trusts			38,753				20,936
Participant loans			2,829,076				2,723,215
Total investments			89,252,658				77,847,692
Receivables:
Company contributions			—				126,623
Participant contributions			6,552				300,864
Other			64,880				4,185
Total receivables			71,432				431,672
Total assets			89,324,090				78,279,364
Liabilities
Refundable contributions			206,334				13,253
Total liabilities			206,334				13,253
Net assets available for benefits		$	89,117,756			$	78,266,111

The accompanying notes are an integral part of these statements.

Flagstar Bank 401(k) Plan

		For the Year Ended
		December 31, 2006
Additions
Additions to net assets attributed to:
Investment income:
Net appreciation in fair value of investments		$	8,519,350
Interest and dividends			1,054,342
Total investment income			9,573,692
Contributions:
Participant			8,593,508
Company			3,119,509
Rollovers			663,159
Total contributions			12,376,176
Total additions			21,949,868
Deductions
Deductions from net assets attributed to:
Participant benefits paid /deemed distributions			11,027,812
Administrative fees			70,411
Total deductions			11,098,223
Net increase			10,851,645
Net assets available for benefits:
Beginning of year			78,266,111
End of year		$	89,117,756

The accompanying notes are an integral part of this statement.

Flagstar Bank 401(k) Plan

Note A — Description of Plan

The following description of the Flagstar Bank 401(k) Plan (the “Plan”) provides only general information. Participants should refer to the Plan document for a more complete description of the Plan’s provisions.

General

The Plan is a defined contribution plan covering all employees of Flagstar Bancorp, Inc. (the “Company”) who have met the eligibility service requirements. An employee is eligible to participate in the Plan after three months of service and is age 21 or older. The Plan is subject to the provisions of the Employee Retirement Income Security Act of 1974 (“ERISA”), as amended.

Contributions

Eligible employees may contribute up to 60% in 2006 and 2005 up to the statutory limits ($15,000 in 2006 and $14,000 in 2005) per annum, of their eligible compensation to the Plan. Participants that meet certain criteria may make additional “catch-up” contributions of up to $5,000 in 2006 and $4,000 in 2005. Participants may also contribute amounts representing rollover contributions from other qualified defined benefit or defined contribution plans. The Company matches employee contributions up to 3% per annum of the employee’s compensation, up to a maximum contribution of $6,600, excluding the catch-up contributions. The Company may make discretionary contributions to the Plan. No discretionary contributions were made in 2006 or 2005. All contributions are invested in accordance with the participant’s directive.

Vesting

Participants are immediately vested in their voluntary contributions. Vesting in the Company contributions and related earnings is based on years of service. A participant becomes 100% vested in Company contributions after five years of credited service.

Participants Accounts

Each participant’s account is credited with the participant’s contribution, the Company contribution made on the employee’s behalf and an allocation of Plan earnings based on the employee’s account balance. The benefit to which a participant is entitled is the benefit that can be provided from the participant’s vested account.

Participant Loans

Participant loans are permitted by the Plan. Participants may borrow a minimum of $1,000 up to the lesser of $50,000 or 50% of the participant’s vested account balance, reduced by the highest outstanding loan balance in the preceding 12 months. All loans must be repaid in level payments through after-tax payroll deductions over a five-year period or up to 10 years for the purchase of a primary residence. The loans are collateralized by up to 50% of a participant’s account balance and bear interest at rates ranging from 5.00% – 9.25%, as determined by the Plan administrator.

Flagstar Bank 401(k) Plan
Notes to Financial Statements — Continued
December 31, 2006 and 2005

Payment of Benefits

Upon termination of services, retirement, attainment of age 59-1/2, death or disability, the participant or his or her beneficiaries are entitled to receive a distribution based on the vested amount of his or her account. A participant may also receive a distribution of his or her vested account balance in the case of financial hardship subject to the discretion of the Plan’s administrator.

Forfeitures

If a participant terminates employment, any non-vested portion of the participant’s account is forfeited. Forfeitures are applied to plan expenses and any amounts remaining are then used to reduce the contributions of the Company. Forfeited non-vested accounts totaled $368,000 at December 31, 2006 and $160,000 at December 31, 2005. In 2006, Company contributions were reduced by $464,000 from forfeited non-vested accounts.

Note B — Summary of Accounting Policies

A summary of the significant accounting polices consistently applied in the preparation of the accompanying financial statements follows.

Basis of Accounting

The accompanying financial statements have been prepared using the accrual method of accounting in accordance with accounting principles generally accepted in the United States of America (U.S. GAAP).

Use of Estimates

The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and changes therein, and the disclosure of contingent assets and liabilities. Actual results could differ from those estimates.

Investment Valuation and Income Recognition

Investments are stated at fair value based upon current quoted market prices. Shares of mutual funds are valued at the net asset value of shares held by the Plan at year end. Participant’s loans are valued at their outstanding balances, which approximates their fair value. Purchases and sales of securities are recorded on a trade-date basis. Interest income is recorded on the accrual basis. Dividends are recorded on the ex-dividend date.

Payment of Benefits

Benefits are recorded when paid.

Flagstar Bank 401(k) Plan
Notes to Financial Statements — Continued
December 31, 2006 and 2005

Note C — Investments

The following presents investments that represent 5% or more of the Plan’s net assets.

December 31, 2006		Number of Shares				Fair Value
Flagstar Bancorp, Inc. Common Stock			868,565			$	12,889,505
Fidelity Retirement Government Money Market Fund			5,754,828				5,754,828
Mutual Funds
Fidelity Growth Company Fund			124,051				8,647,616
Fidelity Dividend Growth Fund			255,708				8,100,816
Fidelity Mid-Cap Stock Fund			257,917				7,515,699
Fidelity Spartan U.S. Equity Index Fund			122,223				6,133,162
Fidelity Diversified International Fund			182,737				6,752,137

December 31, 2005		Number of Shares				Fair Value
Flagstar Bancorp, Inc. Common Stock			859,820			$	12,381,408
Fidelity Retirement Government Money Market Fund			5,207,792				5,207,792
Mutual Funds
Fidelity Growth Company Fund			134,261				8,543,024
Fidelity Dividend Growth Fund			264,514				7,615,354
Fidelity Mid-Cap Stock Fund			245,456				6,521,767
Fidelity Spartan U.S. Equity Index Fund			122,668				5,417,011
Fidelity Diversified International Fund			163,592				5,323,271

During 2006, the Plan’s investments (including gains and losses on investments bought and sold, as well as held during the year) appreciated in value by $8,519,350 as follows:

Flagstar Bancorp, Inc. Common Stock		$	420,610
Mutual funds			8,097,613
Common/Collective Trusts			1,127
Total		$	8,519,350

Note D — Parties-In-Interest

Certain plan investments are shares of mutual funds managed by Fidelity Management Trust Company. Fidelity Management Trust Company is the trustee as defined by the Plan and, therefore, those transactions qualify as party-in-interest transactions. Pursuant to the Plan agreement, the Company may pay a portion of the administrative expenses of the Plan, at its discretion. Expenses paid to the trustee by the Company amounted to $56,000 in 2006. In addition, the Plan trades in the common stock of the Company.

Flagstar Bank 401(k) Plan
Notes to Financial Statements — Continued
December 31, 2006 and 2005

Note E — Plan Termination

Although it has not expressed any intent to do so, the Company has the right under the Plan to discontinue its contributions at any time and to terminate the Plan, subject to provisions of ERISA. In the event of termination of the Plan, the assets of the Plan shall be distributed to all participants to the extent of the value of each participant’s account after adjustment for liquidation expenses, which were not paid by the Company. In the event of the Plan termination, participants would become 100% vested in their Company contributions.

Note F — Tax Status

The Internal Revenue Service has determined and informed the Company by a letter dated January 16, 2002, that the Plan and related trusts are designed in accordance with applicable sections of the Internal Revenue Code (IRC). The Plan was amended, subsequent to the application for favorable determination above, however, the Plan administrator believes that the Plan is designed and is currently being operated in compliance with applicable requirements of the IRC.

Note G — Risks and Uncertainties

The Plan provides for various investment options in any combination of equity securities, bonds, fixed income securities and other investments with market and credit risks. Due to the level of risk associated with certain investment securities, it is at least reasonably possible that changes in the values of investment securities will occur in the near term and that such changes could materially affect participants’ account balances and the amounts reported in the statement of net assets available for benefits.

Note H — Amount Owned to Participants Withdrawing from the Plan

The Plan had no liability to participants who had withdrawn from the Plan as of December 31, 2006 and 2005, respectively.

Note I — Reconciliation of Financial Statements to Form 5500

The following is a reconciliation of statements of net assets available for benefits and the statement of changes in net assets available for benefits per the financial statements to the Form 5500.

		December 31,
		2006				2005
Net assets per financial statements		$	89,117,756			$	78,266,111
Refundable contributions			206,334				13,253
Net assets per Form 5500		$	89,324,090			$	78,279,364
Contributions per financial statements		$	12,376,176			$	12,986,163
Refundable contributions			193,081				13,253
Contributions per Form 5500		$	12,569,257			$	12,999,416

Supplemental Information

Flagstar Bank 401(k) Plan

		(b) Identity of issue, borrower,		(c) Description of investment including maturity date,
(a)		lessor or similar party		rate of interest, collateral, par, or maturity value		(d) Cost		(e) Current value
*		Flagstar Bancorp, Inc		868,565 shares of Common Stock		**		$	12,889,505
		FMTC		Institutional Cash Portfolio		**			1,006,624
		ABF		Large Cap Value Portfolio		**			46,760
		AIM		Small Cap Growth Is		**			145
		AIM		Mid Cap Core Equity Fund – Class A		**			8,726
		AIM		Dynamics Investment Fund		**			67
		AIM		Global Aggressive Growth Class A Fund		**			6,010
		AIM		Basic Value A		**			114
		ALL/BERN		Small/ Mid Cap Val A		**			4,075
		ALLNZ		CCM Mid Cap Administrative Fund		**			6,486
		ALLNZ		NFJ Small Cap Value Fund – Administrative Class		**			147
		AM		Central Ultra Investment Fund		**			4,910
		Ariel		Appreciation Fund		**			34,357
		Ariel		Fund		**			61,316
		Artisan		International Fund		**			33,725
		Artisan		Mid Cap Value Fund		**			31,972
		Baron		Small Cap Fund		**			43,079
		Baron		Asset Fund		**			33,435
		Calvert		New Vision Small Cap Fund - Class A		**			144
		Col/Acorn		Select Fund – Class Z		**			143,393
		Credit Suisse		Global Fixed Income Fund - Common Shares		**			16,177
		Credit Suisse		Large Cap Growth Com		**			4,068
		DWS		International S		**			19,543
		DWS		Global Opps S		**			17,060
		DWS		Dividend High Return Equity Class A		**			3,735
*		Fidelity		Retirement Government Money Market		**			5,754,828
*		Fidelity		Retirement Money Market Portfolio		**			1,095,741
*		Fidelity		Managed Income Portfolio		**			38,750
*		Fidelity		Spartan U.S. Equity Index Fund		**			6,133,162
*		Fidelity		Spartan Total Market Index Fund		**			63,709
*		Fidelity		Spartan Extended Market Index		**			1,445
*		Fidelity		Aggressive International Fund		**			22,596
*		Fidelity		Disciplined Equity Fund		**			71,202
*		Fidelity		Real Estate Investment		**			391,950
*		Fidelity		Large Cap Growth Fund		**			27,635
*		Fidelity		Mid Cap Growth Fund		**			36,063
*		Fidelity		Total Bond Fund		**			476,741
*		Fidelity		Aggressive Growth Fund		**			38,520
*		Fidelity		Balanced Fund		**			567,378
*		Fidelity		Blue Chip Growth Fund		**			44,632
*		Fidelity		Canada Fund		**			267,905
*		Fidelity		Capital & Income Fund		**			100,895
*		Fidelity		Capital Appreciation Fund		**			129,100
*		Fidelity		Dividend Growth Fund		**			8,100,816

Flagstar Bank 401(k) Plan
Schedule H, line 4i — Schedule of Assets (Held at End of Year) — Continued
December 31, 2006

		(b) Identity of issue, borrower,		(c) Description of investment including maturity date,
(a)		lessor or similar party		rate of interest, collateral, par, or maturity value		(d) Cost		(e) Current value
*		Fidelity		Diversified International Fund		**			6,752,137
*		Fidelity		Equity-Income II Fund		**			4,682
*		Fidelity		Equity-Income Fund		**			1,910,270
*		Fidelity		Europe Fund		**			22,968
*		Fidelity		Export and Multinational Fund		**			140,136
*		Fidelity		Fifty Fund		**			2,270
*		Fidelity		Freedom 2000 Fund		**			272,845
*		Fidelity		Freedom 2010 Fund		**			1,374,565
*		Fidelity		Freedom 2020 Fund		**			1,424,331
*		Fidelity		Freedom 2030 Fund		**			1,687,618
*		Fidelity		Freedom 2040 Fund		**			904,035
*		Fidelity		Freedom Income Fund		**			301,063
*		Fidelity		Ginnie Mae Fund		**			33,908
*		Fidelity		Growth Company Fund		**			8,647,616
*		Fidelity		Independence Fund		**			1,639,556
*		Fidelity		International Discovery Fund		**			160,927
*		Fidelity		Japan Fund		**			67,825
*		Fidelity		Low-Priced Stock Fund		**			3,265,510
*		Fidelity		Mid-Cap Stock Fund		**			7,515,699
*		Fidelity		Mortgage Securities Fund		**			1,766
*		Fidelity		New Markets Income Fund		**			210,770
*		Fidelity		Puritan Fund		**			4,258
*		Fidelity		Small Cap Stock Fund		**			68,328
*		Fidelity		Small Capital Retirement Fund		**			1,215,778
*		Fidelity		Trend Fund		**			963
*		Fidelity		U.S. Bond Index Fund		**			2,971,695
*		Fidelity		Value Fund		**			209,017
*		Fidelity		Worldwide Fund		**			777
*		Fidelity		Large Cap Stock Fund		**			13,331
*		Fidelity		Fidelity Fund		**			870
*		Fidelity		Contrafund		**			1,157,721
*		Fidelity		Investment Growth Bond Fund		**			26,979
*		Fidelity		Growth and Income Fund		**			14,823
*		Fidelity		Government Income Fund		**			1,628
*		Fidelity		Overseas Fund		**			27,331
*		Fidelity		Leveraged Company Stock Fund		**			614,197
*		Fidelity		Pacific Basin Fund		**			78,395
*		Fidelity		OTC Portfolio		**			3,626
*		Fidelity		Asset Mgr 50%		**			64,487
*		Fidelity		Asset Mgr 70%		**			7,115
*		Fidelity		INTM Govt Income		**			553
*		Fidelity		Ultrashort Bond		**			5
*		Fidelity		NASDAQ Comp Index		**			28
*		Fidelity		Intl Real Estate		**			157,426

Flagstar Bank 401(k) Plan
Schedule H, line 4i — Schedule of Assets (Held at End of Year) — Continued
December 31, 2006

		(b) Identity of issue, borrower,		(c) Description of investment including maturity date,
(a)		lessor or similar party		rate of interest, collateral, par, or maturity value		(d) Cost		(e) Current value
*		Fidelity		Convertible Securities Fund		**			2,180
*		Fidelity		Utilities Fund		**			221,854
*		Fidelity		Emerging Markets Fund		**			763,767
*		Fidelity		Focused Stock Fund		**			2,039
*		Fidelity		Global Balanced Fund		**			48,699
*		Fidelity		Small Cap Independent Fund		**			31,609
*		Fidelity		Latin America Fund		**			1,435,879
*		Fidelity		Southeast Asia Fund		**			304,339
*		Fidelity		Strategic Income Fund		**			99,392
*		Fidelity		Short Term Bond Fund		**			1,059
*		Fidelity		Large Cap Value Fund		**			73,809
*		Fidelity		Inflation Prot Bond Fund		**			38,379
*		Fidelity		Real Estate Income Fund		**			29,055
*		Fidelity		Blue Chip Value Fund		**			21,400
*		Fidelity		Mid Cap Value Fund		**			4,652
*		Fidelity		Freedom 2005 Fund		**			5,752
*		Fidelity		Freedom 2015 Fund		**			160,989
*		Fidelity		Freedom 2025 Fund		**			111,603
*		Fidelity		Freedom 2035 Fund		**			178,392
*		Fidelity		Europe Cap Appreciation Fund		**			62,818
*		Fidelity		Growth and Income Fund II		**			2,351
*		Fidelity		Strategic Dividend and Income Fund		**			8,089
*		Fidelity		Small Cap Growth Fund		**			15,816
*		Fidelity		Small Cap Value Fund		**			19,576
*		Fidelity		Value Strategies Fund		**			23,319
*		Fidelity		Intermediate Bond Fund		**			6,488
		FMA		Small Company IS		**			6,527
		Franklin		Small-Mid Cap Growth Fund – Class A		**			808
		Hartford		Growth Y Fund		**			7,116
		Hartford		Small Cap Growth Y		**			417
		LD Abbett		Small Cap Build - Class A		**			6,231
		LD Abbett		Affiliated A		**			23,424
		LM		Value Trust Fidelity Class		**			42,610
		LMP		Aggressive Growth A		**			745
		LMP		Large Cap Growth A		**			1,671
		Loomis		Small Cap Value R		**			975
		Managers		Bond Fund		**			5,010
		Managers		Special Equity		**			31
		Managers		Value Fund		**			15,295
		MSI		Emerging Markets Fund – Class B		**			39,905
		MSIFT		High Yield Advance Fund		**			1,098
		MSIFT		MidCap Gth Adv.		**			2,291

Flagstar Bank 401(k) Plan
Schedule H, line 4i — Schedule of Assets (Held at End of Year) — Continued
December 31, 2006

		(b) Identity of issue, borrower,		(c) Description of investment including maturity date,
(a)		lessor or similar party		rate of interest, collateral, par, or maturity value		(d) Cost		(e) Current value
		Mutual		Discovery Fund - Class A		**			119,905
		Mutual		Shares – Class A		**			13,309
		NB		Partners Trust Fund		**			31,038
		NB		International Fund Trust		**			13,816
		The Oakmark		Equity and Income Fund		**			94,859
		The Oakmark		Select I		**			842,142
		The Oakmark		Fund I		**			25,758
		PIM		Global Band AD Unhedged Fund		**			10,451
		PIMCO		High Yield - Administration Class		**			28,134
		PIMCO		Long Term Government - Administrative Class		**			10,605
		PIMCO		Real Return Bond – Admin.		**			1,516
		PIMCO		Total Return Fund - Administrative Class		**			115,064
		Rainier		Small Mid Cap Fund		**			57,819
		Royce		Value Plus Ser		**			92,541
		Royce		Opportunity S Fund		**			12,652
		RS		Partners Fund		**			51,311
		RS		Value Fund		**			10,862
		TCW		Select Equity N Fund		**			16,656
		Templeton		Foreign Fund - Class A		**			61,449
		Templeton		Foreign Small Company - Class A		**			21,620
		Templeton		Dev Markets Fund - Class A		**			43,351
		Templeton		Growth Fund - Class A		**			36,662
		Templeton		World Fund - Class A		**			9,037
		Templeton		Global Bond Fund - Class A		**			26,800
		Touchstn		SC SEL GR Z		**			487
		Van Kampen		Growth and Income Fund - Class A		**			10,783
		Van Kampen		Equity Income – Class A		**			35,675
		WA		Core Plus Bond FI		**			5,500
		West		Asset Core Fidelity Fund		**			1,716
		WFA		Small Cap Value - Class Z		**			29,680
		WFA		C&B Mid Cap Value Fund D		**			6,456
*		Participant Loans		Interest rates ranging from 5% to 9.25% with various
				maturity dates		-0-			2,829,076
								$	89,252,658

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the trustees (or other persons who administer the employee benefit plan) have duly caused this annual report to be signed on its behalf by the undersigned hereunto duly authorized.

EXHIBIT INDEX

Exhibit No.		Description		Page No.
23		Consent of Independent Registered Public Accounting Firm			17