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UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
WASHINGTON, D.C. 20549
FORM 11-K
Mark One
     
þ   ANNUAL REPORT PURSUANT TO SECTION 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
For the fiscal year ended December 31, 2009
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
         
    3  
 
       
Financial Statements
       
 
       
    4  
 
       
    5  
 
       
    6  
 
       
Supplemental Information
       
 
       
    13  
Note: All other schedules required by Section 2520.103-10 of The Department of Labor Rules and Regulations for Reporting and Disclosure under the Employee Retirement Income Security Act of 1974 have been omitted because they are not applicable.
       
 
       
    17  
 
       
Exhibit - 23
       
Consent of Independent Registered Public Accounting Firm
    19  
 EX-23

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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, 2009 and 2008, and the related statement of changes in net assets available for benefits for the year ended December 31, 2009. 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, 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, 2009 and 2008, and the changes in net assets available for benefits for the year ended December 31, 2009, in conformity with accounting principles generally accepted in the United States of America.
Our audits were conducted 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) as of December 31, 2009, is presented for the purpose of additional analysis and is not a required part of the basic 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. The supplemental schedule is the responsibility of the Plan’s management. The supplemental schedule has been subjected to the auditing procedures applied in our audit of the basic 2009 financial statements and, in our opinion, is fairly stated in all material respects in relation to the basic 2009 financial statements taken as a whole.
/s/ Baker Tilly Virchow Krause, LLP
Southfield, Michigan
June 29, 2010

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Flagstar Bank 401(k) Plan
Statements of Net Assets Available for Benefits
                 
    December 31,  
    2009     2008  
Assets
               
Investments — at fair value
               
Flagstar Bancorp, Inc. common stock
  $ 3,281,192     $ 3,041,504  
Mutual funds
    67,385,569       46,463,706  
Money market funds
    8,850,847       9,351,460  
Common collective trust fund
    59,217       222,661  
Participant loans
    3,191,386       3,286,426  
       
Total investments – at fair value
    82,768,211       62,365,757  
Other
    86,388       936  
       
Total assets
    82,854,599       62,366,693  
       
Liabilities
               
Refundable contributions
    169,307       108,374  
       
Total liabilities
    169,307       108,374  
Net assets available for benefits reflecting all investments at fair value
    82,685,292       62,258,319  
 
               
Adjustment from fair value to contract value for interest in common collective trust fund relating to fully benefit – responsive investment contracts
    10,909       11,855  
       
Net assets available for benefits
  $ 82,696,201     $ 62,270,174  
       
The accompanying notes are an integral part of these statements.

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Flagstar Bank 401(k) Plan
Statement of Changes in Net Assets Available for Benefits
         
    For the Year Ended  
    December 31, 2009  
Additions        
Additions to net assets attributed to:
       
Net realized and unrealized appreciation in fair value of investments
  $ 15,644,052  
Interest
    248,599  
Dividends
    967,524  
 
     
Total investment income
    16,860,175  
 
     
Contributions:
       
Participant
    10,097,358  
Company
    3,129,786  
Rollovers
    194,358  
 
     
Total contributions
    13,421,502  
 
     
Total additions
    30,281,677  
 
     
Deductions
       
Deductions from net assets attributed to:
       
Participant benefits paid /deemed distributions
    9,748,011  
Administrative fees
    107,639  
 
     
Total deductions
    9,855,650  
 
     
Net increase
    20,426,027  
Net assets available for benefits:
       
Beginning of year
    62,270,174  
 
     
End of year
  $ 82,696,201  
 
     
The accompanying notes are an integral part of these statements.

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Flagstar Bank 401(k) Plan
Notes to Financial Statements
December 31, 2009 and 2008
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 available to all employees of Flagstar Bancorp, Inc. (the “Company”) who have met the eligibility service requirements. The Plan includes a salary deferral feature under section 401(k) of the Internal Revenue Code (“IRC”). 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% of their eligible compensation to the Plan in 2009 not to exceed the annual Internal Revenue Service (“IRS”) dollar limitation of $16,500. Participants were also able to make additional contributions of up to $5,500 the annual IRS dollar limit on “catch-up” contributions in 2009. Certain participants were also able to contribute amounts representing rollover contributions from other qualified defined benefit or defined contribution plans. In 2009, the Plan was amended to suspend all employer matching contributions effective October 1, 2009 until such time as the Company affirmatively reinstates such matching contributions. The Company may make discretionary contributions to the Plan. No discretionary contributions were made in 2009. All contributions are invested in accordance with the participant’s directive.
     Vesting
Participants are immediately vested in their voluntary contributions and related earnings. 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 participant’s share of net earnings or losses of their respective elected investment options. 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 4.25% to 9.25%, as determined by the Plan administrator at the date of issuance of the loan.
     Investment Options
Upon enrollment in the Plan, a participant may direct contributions in 1% increments in any of the available investment options. Participants may change their designation daily.
     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 or rollover to an IRA or other eligible plan a single lump sum

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Flagstar Bank 401(k) Plan
Notes to Financial Statements — Continued
December 31, 2009 and 2008
amount equal to 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 $216,000 at December 31, 2009. In 2009, Company contributions were reduced by $343,000 and administrative expenses were reduced by $13,000 from forfeited non-vested accounts.
     Administrative Expenses
The Company pays a portion of the Plan’s administrative expenses. Participants pay the applicable fees associated with their loans distributions, withdrawals and stock transactions.
     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 the IRC and 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 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 amounts reported in the financial statements and accompanying notes. Actual results could differ from those estimates.
     Investment Valuation and Income Recognition
Investments are stated at fair value using the methods described in Note C. The Statement of Changes in Net Assets Available for Benefits is presented on a contract value basis. 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.
     Fidelity Managed Income Portfolio
The Plan has an investment in the Managed Income Portfolio, a common trust fund of the Fidelity Group Trust for the Employee Benefit Plans (the “Managed Income Portfolio Fund”), which includes benefit-responsive investment contracts. Investment contracts held by a defined-contribution plan are required to be reported at fair value. However, contract value is the relevant measurement attribute for that portion of the net assets available for benefits of a defined-contribution plan attributable to fully benefit-responsive investment contracts because the contract value is the amount participants would receive if they were to initiate permitted transactions under the terms of the Plan. Contract value represents contributions plus earnings, less participants withdrawals and administrative

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Flagstar Bank 401(k) Plan
Notes to Financial Statements — Continued
December 31, 2009 and 2008
expenses. The statements of assets available for benefits present the fair value of the Managed Income Portfolio Fund and the adjustment from fair value to contract value.
The fair value of the Plan’s investment in the Managed Income Portfolio Fund was $59,217 and $222,661 as December 31, 2009 and 2008, respectively. The contract value of the Plan’s investment in the Managed Income Portfolio Fund was $70,216 and $234,516 as of December 31, 2009 and 2008, respectively..
     Payment of Benefits
Benefits are recorded when paid.
     Subsequent Events
Management evaluates the impact of all subsequent events through the issuance date of the Plan’s financial statements for the year ended December 31, 2009. Management has evaluated subsequent events through June 29, 2010, and has determined that all subsequent events have been appropriately recognized and disclosed in the accompanying financial statements.
Note C — Fair Value Accounting
The Plan assets, which are recorded at fair value, are grouped into three levels based on the markets in which the assets are traded and the reliability of the assumptions used to determined fair value. An asset’s level within the fair value hierarchy is based on the lowest level of input that is significant to the fair value measurement (with Level 1 considered highest and Level 3 considered lowest). A brief description of each level follows:
    Level 1 — Fair value is based upon quoted prices for identical instruments in active markets.
 
    Level 2 — Fair value is based upon quoted prices for similar instruments in active markets, quoted prices for identical or similar instruments in markets that are not active, and model-based valuation techniques for which all significant assumptions are observable in the market.
 
    Level 3 — Fair value is generated from model-based techniques that use at least one significant assumption not observable in the market. These unobservable assumptions reflect estimates that market participants would use in pricing that asset or liability. Valuation techniques may include discounted cash flow models and similar techniques.
The following is a description of the valuation methodologies used by the Plan for instruments measured at fair value, as well as the general classification of such instruments pursuant to the valuation hierarchy.
Flagstar Bancorp common stock: Valued at the closing price reported on the active market on which the security is traded.
Mutual funds: Valued at the net asset value of the shares held by the Plan at year end.
Money market funds: Valued at cost which approximates the net asset value of the shares held by the Plan at year end.
Common collective trust fund: Valued as the sum of (a) the fair value of the investments in guaranteed investment contracts (traditional GICs) and security-backed investment contracts that are wrapped by an insurance company, bank or other financial institution as determined by that fund’s trustee (synthetic GICs) and (b) the fair value of the fund’s investments in externally managed collective investment funds as determined by those funds’ trustees.
Participant loans: Valued at the amortized cost plus accrued interest, which approximates fair value. The methods described above may produce a fair value estimate that may not be indicative of net realizable value or reflective of future fair values. Furthermore, while the Plan believes its valuation methods are appropriate and consistent with other market participants, the use of different methodologies or assumptions to determine the fair

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Flagstar Bank 401(k) Plan
Notes to Financial Statements — Continued
December 31, 2009 and 2008
value of certain financial instruments could result in different estimates of fair values of the same financial instruments at the reporting date.
The following tables presents the Plans investments carried at fair value as of December 31, 2009 and 2008, by valuation hierarchy (as described above):
                                 
                            Investments at Fair  
December 31, 2009   Level 1     Level 2     Level 3     Value  
     
Flagstar Bancorp common stock
  $ 3,281,192     $     $     $ 3,281,192  
Mutual funds
    67,385,569                   67,385,569  
Money market funds
          8,850,847             8,850,847  
Common collective trust fund
          59,217             59,217  
Participant loans
                3,191,386       3,191,386  
     
 
                               
Total assets at fair value
  $ 70,666,761     $ 8,910,064     $ 3,191,386     $ 82,768,211  
     
                                 
                            Investments at Fair  
December 31, 2008   Level 1     Level 2     Level 3     Value  
     
Flagstar Bancorp common stock
  $ 3,041,504     $     $     $ 3,041,504  
Mutual funds
    46,463,706                   46,463,706  
Money market funds
          9,351,460             9,351,460  
Common collective trust fund
          222,661             222,661  
Participant loans
                3,286,426       3,286,426  
     
 
                               
Total assets at fair value
  $ 49,505,210     $ 9,574,121     $ 3,286,426     $ 62,365,757  
     
The following table provides a summary of changes in the fair value of the Plan’s level 3 assets for the year ended December 31, 2009.
         
    Participant  
    Loans  
Balance — January 1, 2009
  $ 3,286,426  
New loans issued, interest earned and repayments, net
    (95,040 )
 
     
Balance — December 31, 2009
  $ 3,191,386  
 
     
Note D — Investments
The following presents investments that represent 5% or more of the Plan’s net assets.
                 
    Number of        
December 31, 2009   Shares     Fair Value  
 
Fidelity Retirement Government Money Market Fund
    7,047,420     $ 7,047,420  
Mutual Funds
               
Fidelity Growth Company Fund
    116,530       8,038,269  
Fidelity Dividend Growth Fund
    306,698       7,259,548  
Fidelity Diversified International Fund
    238,388       6,674,874  
Fidelity Mid-Cap Stock Fund
    278,683       6,526,755  
Fidelity U.S. Bond Index Funds
    395,110       4,369,913  
Fidelity Spartan U.S. Equity Index Fund
    109,134       4,303,173  

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Flagstar Bank 401(k) Plan
Notes to Financial Statements — Continued
December 31, 2009 and 2008
                 
    Number of        
December 31, 2008   Shares     Fair Value  
 
Fidelity Retirement Government Money Market Fund
    7,736,897     $ 7,736,897  
Mutual Funds
               
Fidelity Growth Company Fund
    112,779       5,521,645  
Fidelity Diversified International Fund
    212,612       4,573,293  
Fidelity Dividend Growth Fund
    288,659       4,557,920  
Fidelity Mid-Cap Stock Fund
    262,787       4,102,097  
Fidelity U.S. Bond Index Funds
    355,627       3,837,215  
Fidelity Spartan U.S. Equity Index Fund
    104,380       3,329,709  
During 2009, the Plan’s investments (including gains and losses on investments bought and sold, as well as held during the year) appreciated in fair value as determined by quoted market prices as follows:
         
    Net Realized and  
    Unrealized  
    Appreciation  
    (Depreciation), in  
    fair value of  
Flagstar Bancorp, Inc. common stock
  $ (677,645 )
Mutual funds
    16,321,697  
 
     
Total
  $ 15,644,052  
 
     
Note E — 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 $53,000 in 2009. In addition, the Plan trades in the common stock of the Company.
The Plan held 5,468,654 and 4,283,809 shares of Flagstar Bancorp, Inc. common stock as of December 31, 2009 and 2008, respectively. During 2009, Flagstar Bancorp, Inc. did not declare or pay any common stock dividends.
Note F Tax Status
The Internal Revenue Service has determined and informed the Company by a letter dated December 5, 2001, 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 financial statements.

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Flagstar Bank 401(k) Plan
Notes to Financial Statements — Continued

December 31, 2009 and 2008
Note H— Amounts Owed to Participants Withdrawing from the Plan
The Plan had no liability to participants who had withdrawn from the Plan as of December 31, 2009 and 2008, respectively.
Note I— Reconciliation of Financial Statements to Form 5500
The following is a reconciliation of statements of net assets available for benefits per the financial statements to the 2009 Form 5500.
                 
    December 31,  
    2009     2008  
     
Net assets available for benefits per financial statements
  $ 82,696,201     $ 62,270,174  
Adjustment to fair value from contract-value for investment relating to fully benefit-responsive investment contracts
    (10,909 )     (11,855 )
     
Net assets available for benefits per Form 5500
  $ 82,685,292     $ 62,258,319  
     
The following is a reconciliation of the activity reported within the statement of changes in net assets available for benefits per the financial statements to the 2009 Form 5500.
         
    December 31, 2009  
Contributions per financial statements
  $ 13,421,502  
Refundable contributions
    (169,307 )
 
     
Contributions per Form 5500
  $ 13,252,195  
 
     
 
Net increase in net assets available for benefits per Financial Statements
  $ 20,426,027  
Change in adjustment to fair value from contract value for investment relating to fully benefit investment contracts
    946  
 
     
Net income per Form 5500
  $ 20,426,973  
 
     

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Supplemental Information

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Flagstar Bank 401(k) Plan
Schedule H, line 4i — Schedule of Assets (Held at End of Year)
December 31, 2009
                     
        (c) Description of investment including        
    (b) Identity of issue, borrower,   maturity date, rate of interest,        
(a)   lessor or similar party   collateral, par, or maturity value   (d) Cost   (e) Current value
 
Common Stock                
*
  Flagstar Bancorp, Inc   5,468,654 shares of Common Stock   **   $ 3,281,192  
 
                   
Mutual Funds                
 
  ABDN   Glbl FX Inc Is   **     18,522  
 
  ABF   International Equity Investment   **     10,741  
 
  ABF   Large Cap Value Portfolio   **     48,750  
 
  AIM   Basic Value A   **     2,548  
 
  AIM   Constellation Class A   **     853  
 
  AIM   Dynamics Investment Fund   **     299  
 
  AIM   Global Small and Mid Cap Growth A   **     17,305  
 
  AIM   Mid Cap Core Equity Fund — Class A   **     41,514  
 
  AIM   Small Cap Growth Is   **     471  
 
  ALL/BERN   Small/ Mid Cap Val A   **     1,947  
 
  ALLNZ   CCM Mid Cap Administrative Fund   **     1,461  
 
  ALLNZ   NFJ Small Cap Value Fund — Administrative Class   **     468  
 
  AM   CEN LG CO VAL INV   **     157  
 
  AM   CENT VISTA INV   **     10,329  
 
  AM   Central Ultra Investment Fund   **     4,983  
 
  Ariel   Appreciation Fund   **     73,256  
 
  Ariel   Fund   **     42,920  
 
  Artisan   International Fund   **     107,564  
 
  Artisan   Mid Cap Value Fund   **     38,600  
 
  Baron   Asset Fund   **     33,915  
 
  Baron   Small Cap Fund   **     61,222  
 
  Calvert   Cap Acc A   **     286  
 
  Calvert   SIF Equity A   **     82  
 
  Col   Consolidated High Yield Z   **     310  
 
  Col/Acorn   Select Fund — Class Z   **     79,755  
 
  Credit Suisse   Large Cap Growth Com   **     3,655  
 
  Credit Suisse   Mid Cap Core Com   **     446  
 
  DOMINI   Social Eq Inv   **     647  
 
  DWS   Global Opps S   **     22,251  
 
  DWS   International S   **     5,304  
 
  DWS   Strategic Val A   **     2,719  
*
  Fidelity   Asset Mgr 20%   **     81  
*
  Fidelity   Asset Mgr 50%   **     12,641  
*
  Fidelity   Asset Mgr 70%   **     15,232  
*
  Fidelity   Asset Mgr 85%   **     10,782  
*
  Fidelity   Balanced Fund   **     97,752  
*
  Fidelity   Blue Chip Growth Fund   **     101,747  
*
  Fidelity   Blue Chip Value Fund   **     26,661  
*
  Fidelity   Canada Fund   **     416,300  
*
  Fidelity   Capital & Income Fund   **     171,913  
*
  Fidelity   Capital Appreciation Fund   **     30,269  
*
  Fidelity   Contra-fund   **     1,300,265  
*
  Fidelity   Convertible Securities Fund   **     9,018  
*
  Fidelity   Disciplined Equity Fund   **     66,413  
*
  Fidelity   Diversified International Fund   **     6,674,874  
*
  Fidelity   Dividend Growth Fund   **     7,259,548  
*
  Fidelity   Emerging Markets Fund   **     396,726  
*
  Fidelity   Equity-Income Fund   **     1,978,588  
*
  Fidelity   Equity-Income II Fund   **     2,870  
*
  Fidelity   Europe Cap Appreciation Fund   **     17,005  

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Flagstar Bank 401(k) Plan
Schedule H, line 4i — Schedule of Assets (Held at End of Year)
December 31, 2009
                     
        (c) Description of investment including        
    (b) Identity of issue, borrower,   maturity date, rate of interest,        
(a)   lessor or similar party   collateral, par, or maturity value   (d) Cost   (e) Current value
 
*
  Fidelity   Europe Fund   **     33,321  
*
  Fidelity   Export and Multinational Fund   **     69,199  
*
  Fidelity   Fidelity Fund   **     46,020  
*
  Fidelity   Fifty Fund   **     11,599  
*
  Fidelity   Focused High Inc   **     2,688  
*
  Fidelity   Focused Stock Fund   **     31,133  
*
  Fidelity   Freedom 2000 Fund   **     345,676  
*
  Fidelity   Freedom 2005 Fund   **     18,152  
*
  Fidelity   Freedom 2010 Fund   **     1,159,583  
*
  Fidelity   Freedom 2015 Fund   **     279,402  
*
  Fidelity   Freedom 2020 Fund   **     2,210,403  
*
  Fidelity   Freedom 2025 Fund   **     375,092  
*
  Fidelity   Freedom 2030 Fund   **     2,185,663  
*
  Fidelity   Freedom 2035 Fund   **     757,902  
*
  Fidelity   Freedom 2040 Fund   **     1,661,060  
*
  Fidelity   Freedom 2045   **     138,818  
*
  Fidelity   Freedom 2050   **     257,599  
*
  Fidelity   Freedom Income Fund   **     555,027  
*
  Fidelity   Ginnie Mae Fund   **     179,152  
*
  Fidelity   Global Balanced Fund   **     4,527  
*
  Fidelity   Government Income Fund   **     372,009  
*
  Fidelity   GR Strategies   **     33,748  
*
  Fidelity   Growth and Income Fund   **     30,556  
*
  Fidelity   Growth Company Fund   **     8,038,269  
*
  Fidelity   Independence Fund   **     1,942,045  
*
  Fidelity   Inflation Prot Bond Fund   **     46,462  
*
  Fidelity   Institutional Shares Int Govt   **     18,872  
*
  Fidelity   Intermediate Bond Fund   **     12,048  
*
  Fidelity   Intermediate Government Income   **     104,389  
*
  Fidelity   International Cap Appreciation   **     13,112  
*
  Fidelity   International Discovery Fund   **     156,201  
*
  Fidelity   Intl Real Estate   **     108,413  
*
  Fidelity   Investment Growth Bond Fund   **     13,712  
*
  Fidelity   Japan Fund   **     17,559  
*
  Fidelity   Large Cap Growth Fund   **     22,409  
*
  Fidelity   Large Cap Stock Fund   **     137,101  
*
  Fidelity   Large Cap Value Fund   **     69,916  
*
  Fidelity   Latin America Fund   **     1,071,847  
*
  Fidelity   Leveraged Company Stock Fund   **     618,217  
*
  Fidelity   Low-Priced Stock Fund   **     1,870,721  
*
  Fidelity   Mega Cap Stock   **     23,971  
*
  Fidelity   Mid Cap Growth Fund   **     14,893  
*
  Fidelity   Mid Cap Value Fund   **     44,807  
*
  Fidelity   Mid-Cap Stock Fund   **     6,526,755  
*
  Fidelity   Mortgage Securities Fund   **     7,321  
*
  Fidelity   NASDAQ Comp Index   **     3,552  
*
  Fidelity   New Markets Income Fund   **     246,333  
*
  Fidelity   OTC Portfolio   **     80,785  
*
  Fidelity   Overseas Fund   **     178,060  
*
  Fidelity   Pacific Basin Fund   **     32,684  
*
  Fidelity   Puritan Fund   **     17,962  
*
  Fidelity   Real Estate Income Fund   **     88,340  
*
  Fidelity   Real Estate Investment   **     127,289  
*
  Fidelity   Short Term Bond Fund   **     6,824  
*
  Fidelity   Small Cap Discovery   **     1,818,969  

14


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Flagstar Bank 401(k) Plan
Schedule H, line 4i — Schedule of Assets (Held at End of Year)
December 31, 2009
                     
        (c) Description of investment including        
    (b) Identity of issue, borrower,   maturity date, rate of interest,        
(a)   lessor or similar party   collateral, par, or maturity value   (d) Cost   (e) Current value
 
*
  Fidelity   Small Cap Growth Fund   **     18,742  
*
  Fidelity   Small Cap Independent Fund   **     17,985  
*
  Fidelity   Small Cap Stock Fund   **     71,191  
*
  Fidelity   Small Cap Value Fund   **     34,211  
*
  Fidelity   Southeast Asia Fund   **     226,624  
*
  Fidelity   Spartan U.S. Equity Index Fund   **     4,303,173  
*
  Fidelity   Stock Selector   **     11,952  
*
  Fidelity   Strategic Dividend and Income Fund   **     2,159  
*
  Fidelity   Strategic Income Fund   **     121,406  
*
  Fidelity   Telcom and Utilities Fund   **     201,880  
*
  Fidelity   Total Bond Fund   **     24,748  
*
  Fidelity   Trend Fund   **     18,434  
*
  Fidelity   U.S. Bond Index Fund   **     4,369,913  
*
  Fidelity   Ultrashort Bond   **     2,730  
*
  Fidelity   Value Fund   **     133,274  
*
  Fidelity   Value Strategies Fund   **     100,293  
*
  Fidelity   Worldwide Fund   **     4,808  
 
  Franklin   Small-Mid Cap Growth Fund — Class A   **     7,457  
 
  Hartford   Growth Y   **     5,018  
 
  Hartford   International Growth Y   **     641  
 
  JH   Small Company A   **     18,565  
 
  LD Abbett   Affiliated A   **     50,585  
 
  LD Abbett   Small Cap Build — Class A   **     48,196  
 
  LM   CBA AGG GR A   **     58,604  
 
  LM   CBA LC GRO A   **     2,058  
 
  LM   Value Trust Fidelity Class   **     18,752  
 
  Loomis   Growth A   **     1,587  
 
  Loomis   Small Cap Value R   **     4,031  
 
  Managers   AMG ES LG CP GR   **     37  
 
  Managers   Bond Fund   **     129,326  
 
  Managers   Special Equity   **     3,461  
 
  MSIF   Capital Growth P   **     6,511  
 
  MSIF   Intl Equity P   **     682  
 
  MSIF   Value P   **     863  
 
  MSIFT   Emerging Markets P   **     63,600  
 
  MSIFT   Mid Cap Growth P   **     21,548  
 
  Mutual   Global Discovery Fund — Class A   **     114,508  
 
  Mutual   Shares — Class A   **     48,757  
 
  NB   Core Fund Inv   **     5,795  
 
  NB   Genesis — Investment Class   **     2,793  
 
  NB   Guardian Trust   **     178  
 
  NB   High Income Bond Investment   **     37,409  
 
  NB   International Fund Trust   **     18,035  
 
  NB   Partners Trust Fund   **     5,243  
 
  NB   Regency Trust   **     251  
 
  NB   Socially Responsible Trust   **     304  
 
  PIM   Global Band AD Un-hedged Fund   **     47,958  
 
  PIMCO   High Yield — Administration Class   **     12,920  
 
  PIMCO   Long Term Government — Administrative Class   **     50,853  
 
  PIMCO   Low DUR Administration Fund   **     45,230  
 
  PIMCO   Real Return Bond — Admin.   **     158,241  
 
  PIMCO   Total Return Fund — Administrative Class   **     670,662  
 
  Rainier   Small Mid Cap Fund   **     91,978  
 
  Royce   Total Return SER   **     4,254  
 
  Royce   Value Plus Ser   **     155,264  

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Flagstar Bank 401(k) Plan
Schedule H, line 4i — Schedule of Assets (Held at End of Year)
December 31, 2009
                     
        (c) Description of investment including        
    (b) Identity of issue, borrower,   maturity date, rate of interest,        
(a)   lessor or similar party   collateral, par, or maturity value   (d) Cost   (e) Current value
 
 
  RS   Partners Fund A   **     32,917  
 
  RS   Small Cap Grth A   **     3,187  
 
  RS   Value Fund   **     17,945  
 
  SPTN   Extended Market Index   **     53,967  
 
  SPTN   Total Market Index   **     84,588  
 
  TCW   Select Equity N   **     41  
 
  Templeton   Dev Markets Fund — Class A   **     191,226  
 
  Templeton   Foreign Fund — Class A   **     128,292  
 
  Templeton   Foreign Small Company — Class A   **     19,953  
 
  Templeton   Global Bond Fund — Class A   **     239,259  
 
  Templeton   Growth Fund — Class A   **     17,513  
 
  Templeton   World Fund — Class A   **     6,131  
 
  The Oakmark   Equity and Income Fund   **     192,406  
 
  The Oakmark   Fund I   **     36,971  
 
  The Oakmark   Select I   **     1,122,839  
 
  Touchstone   SC SEL GR Z   **     34,718  
 
  Van Kampen   Equity Income — Class A   **     52,766  
 
  Van Kampen   Growth and Income Fund — Class A   **     20,207  
 
  Virtus   Mid Cap Value A   **     15,560  
 
  WA   Core Plus Bond Fi   **     139  
 
  WEST   Asset Core Fi   **     2  
 
  WFA   C&B Mid Cap Value Fund D   **     637  
 
  WFA   Mid Cap DSCPLD Investment   **     376  
 
  WFA   Small Cap Value Investment   **     77,912  
 
  WFA   Small Co Value A   **     207  
 
                 
 
 
      Total Mutual Funds         67,385,569  
 
                   
Money Market Funds                
*
      Fidelity   Retirement Government Money Market   **     7,047,420  
*
      Fidelity   Retirement Money Market Portfolio   **     1,577,313  
*
      FMTC   Institutional Cash Portfolio   **     226,114  
 
                 
 
 
      Total Money Market Funds         8,850,847  
 
                   
Common Collective Trust Fund                
*
      Fidelity   Managed Income Portfolio   **     59,217  
 
                   
Participant Loans                
*
      Participant Loans   Interest rates ranging from 4.25% to 9.25% with various maturity dates         3,191,386  
 
                 
 
                   
 
      Total Investments       $ 82,768,211  
 
                 
 
*   Party-in-interest to the Plan
 
**   Participant Directed

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SIGNATURE
Pursuant to the requirements of the Securities Exchange Act of 1934, the trustees (or other persons who administer the employee benefit plan) who is duly authorized by the Company have signed this annual report on the Plan’s behalf.
         
  FLAGSTAR BANK 401(k) PLAN
 
 
June 29, 2010  By:   /s/ Rebecca A. Lucci    
    Plan Administrator   
       
 

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EXHIBIT INDEX
             
Exhibit No.   Description   Page No.
 
           
23
  Consent of Independent Registered Public Accounting Firm     19  

18