e11vk
Table of Contents

 
 
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, 2006
OR
     
o   TRANSITION REPORT PURSUANT TO SECTION 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
For the transition period from                      to
Commission File No. 0-2989
A. Full title of the plan and the address of the plan, if different from that of the issuer named below:
COMMERCE BANCSHARES PARTICIPATING INVESTMENT PLAN
B. Name of issuer of the securities held pursuant to the plan and the address of its principal executive office:
COMMERCE BANCSHARES, INC.
1000 Walnut, Kansas City, MO 64106
 
 

 


 

COMMERCE BANCSHARES PARTICIPATING INVESTMENT PLAN
TABLE OF CONTENTS
     
    Page Number
  2
 
   
Financial Statements:
   
  4
  5
  6
 
   
Supplemental Schedules:
   
  14
  15
Consent of Independent Registered Public Accounting Firm
   
 Consent of Independent Registered Public Accounting Firm
 Consent of Independent Registered Public Accounting Firm
SIGNATURES
The Plan. 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.
             
    COMMERCE BANCSHARES    
    PARTICIPATING INVESTMENT PLAN    
 
           
 
  By:   /s/ Jeffery D. Aberdeen
 
   
    Jeffery D. Aberdeen    
    Co-Chairperson, Retirement Committee    
 
           
 
  By:   /s/ Sara E. Foster    
 
           
    Sara E. Foster    
    Co-Chairperson, Retirement Committee    
Date: June 22, 2007

 


Table of Contents

REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM
The Retirement Committee of Commerce Bancshares, Inc.
Commerce Bancshares Participating Investment Plan:
We have audited the accompanying statements of net assets available for benefits of the Commerce Bancshares Participating Investment Plan (the Plan) as of December 31, 2006 and 2005, and the related statements of changes in net assets available for benefits for the years ended December 31, 2006 and 2005. 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. An audit 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 its net assets available for benefits for the years ended December 31, 2006 and 2005, in conformity with U.S. generally accepted accounting principles.
Our audits were conducted for the purpose of forming an opinion on the basic financial statements taken as a whole. The accompanying supplemental schedules of schedule H, line 4i – schedule of assets (held at end of year) as of December 31, 2006 and schedule H, line 4j – schedule of reportable transactions for the year ended December 31, 2006 are presented for the purpose of additional analysis and are not a required part of the basic financial statements, but are supplementary information required by the Department of Labor’s Rules and Regulations for Reporting and Disclosure under the Employee Retirement Income Security Act of 1974. The supplemental schedules are the responsibility of the Plan’s management. The supplemental schedules have been subjected to the auditing procedures applied in the audits of the basic financial statements and, in our opinion, are fairly stated in all material respects in relation to the basic financial statements taken as a whole.
/s/ Mayer Hoffman McCann P.C.
Leawood, Kansas
June 22, 2007

2


Table of Contents

REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM
The Retirement Committee of Commerce Bancshares, Inc.
Commerce Bancshares Participating Investment Plan:
We have audited the accompanying statement of changes in net assets available for benefits of the Commerce Bancshares Participating Investment Plan (the Plan) for the year ended December 31, 2004. This financial statement is the responsibility of the Plan’s management. Our responsibility is to express an opinion on this financial statement based on our audit.
We conducted our audit in accordance with the standards of the Public Company Accounting Oversight Board (United States). Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement. 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 audit provides a reasonable basis for our opinion.
In our opinion, the financial statement referred to above presents fairly, in all material respects, the changes in net assets available for benefits of the Plan for the year ended December 31, 2004, in conformity with U.S. generally accepted accounting principles.
/s/ KPMG LLP
Kansas City, Missouri
June 22, 2005

3


Table of Contents

COMMERCE BANCSHARES PARTICIPATING INVESTMENT PLAN
Statements of Net Assets Available for Benefits
December 31, 2006 and 2005
                 
    2006     2005  
ASSETS
               
 
               
Cash, non-interest bearing
  $ 68     $ 425  
 
           
 
               
Investments, at fair value:
               
Commerce Bancshares, Inc. Common Stock Fund
    162,078,256       170,853,461  
Mutual funds
    155,705,386       126,839,410  
Loans to participants
    6,709,893       6,469,136  
 
           
Total investments
    324,493,535       304,162,007  
 
           
 
               
Contributions receivable:
               
Employer
          28,165  
 
           
Total contributions receivable
          28,165  
 
           
 
               
Total assets
    324,493,603       304,190,597  
 
           
 
               
LIABILITIES
               
 
               
Due to participants
          28,165  
 
           
 
               
Total liabilities
          28,165  
 
           
 
               
Net assets available for benefits
  $ 324,493,603     $ 304,162,432  
 
           
See accompanying notes to financial statements

4


Table of Contents

COMMERCE BANCSHARES PARTICIPATING INVESTMENT PLAN
Statements of Changes in Net Assets Available for Benefits
Years ended December 31, 2006, 2005, and 2004
                         
    2006     2005     2004  
Additions to Net Assets Attributable to:
                       
Investment income:
                       
Interest
  $ 1,138,747     $ 677,699     $ 180,259  
Dividends
    5,824,799       4,096,931       2,119,963  
Interest income on loans to participants
    437,355       351,243       332,858  
Net appreciation in fair value of investments
    6,128,545       16,394,800       16,472,314  
 
                 
 
                       
Total investment income
    13,529,446       21,520,673       19,105,394  
 
                 
 
                       
Contributions:
                       
Participant
    15,293,058       14,043,183       12,889,584  
Employer
    8,056,387       7,671,559       4,188,344  
Participant rollover
    658,050       1,199,452       1,044,938  
 
                 
 
                       
Total contributions
    24,007,495       22,914,194       18,122,866  
 
                 
 
                       
Total additions
    37,536,941       44,434,867       37,228,260  
 
                 
 
                       
Deductions from Net Assets Attributable to:
                       
Distributions to participants
    (17,170,276 )     (26,053,222 )     (23,046,883 )
Administrative expenses
    (35,494 )     (27,792 )     (19,477 )
 
                 
 
                       
Total deductions
    (17,205,770 )     (26,081,014 )     (23,066,360 )
 
                 
 
                       
Net increase
    20,331,171       18,353,853       14,161,900  
Net assets available for benefits:
                       
Beginning of year
    304,162,432       285,808,579       271,646,679  
 
                 
 
                       
End of year
  $ 324,493,603     $ 304,162,432     $ 285,808,579  
 
                 
See accompanying notes to financial statements

5


Table of Contents

COMMERCE BANCSHARES PARTICIPATING INVESTMENT PLAN
Notes to Financial Statements
December 31, 2006, 2005, and 2004
(1)   Description of the Plan
 
    General
 
    The following description of the Commerce Bancshares Participating Investment Plan (the Plan) is provided for general informational purposes only. Terms of the Plan are more fully described in the Plan document, which is available to each participant. The Plan is a defined contribution plan that is qualified under section 401 of the Internal Revenue Code and covers employees of Commerce Bancshares, Inc. (the Company) or a participating subsidiary who are 21 years or older. Employees are eligible to participate as of January 1, April 1, July 1, or October 1 following the completion of thirty days of service. The Plan is subject to the provisions of the Employee Retirement Security Act of 1974 (ERISA).
 
    The Company is the plan sponsor and is advised by the Retirement Committee of Commerce Bancshares, Inc., which acts as the plan administrator. Commerce Bank, N.A., a subsidiary of the Company, is the trustee of the Plan. State Street Bank and Trust Co. and AON Consulting, Inc. performed recordkeeping and custodial services for the Plan until July 1, 2004 when the Plan’s custodian and record keeping services were assumed by Fidelity Investments. There were 4,117 and 4,001 participants with balances in the Plan at December 31, 2006 and 2005, respectively.
 
    Contributions
 
    Participating employees may elect to contribute to the Plan a maximum of 25% of their eligible compensation, as defined by the Plan, and subject to certain limitations under the Internal Revenue Code (not to exceed $15,000, $14,000 and $13,000 in 2006, 2005 and 2004, respectively). Additionally, participants who attained the age of 50 during 2006, 2005 or 2004 could contribute an additional $5,000, $4,000, or $3,000 of catch-up contributions, respectively. The catch-up contributions are not subject to the employer matching contribution. All participant contributions are made on a pretax basis.
 
    Throughout 2004 the Company and participating subsidiaries contributed a matching contribution equal to 50% of the first 6% of eligible compensation. Effective January 1, 2005 this was changed to a graded matching percentage from 50% — 100% determined by age plus years of employment on the first 7% of eligible compensation. Additionally, the Plan was amended to allow the Company to make a discretionary contribution. For the years ended December 31, 2006 and 2005, the Company did not make a discretionary contribution. Participants may make a deferral contribution over 7%, which is not considered in determining Company contributions, for a maximum 25% pre-tax contribution.
 
    Through June 2004, participants had the option to direct the investment of their contributions and the matching employer’s contributions (except as described in note 4) in any combination of the Commerce Bancshares, Inc. Common Stock Fund (Company Stock Fund), Commerce Asset Allocation Fund, Commerce Bond Fund, Commerce Growth Fund, Commerce International Equity Fund, Commerce MidCap Fund, Commerce Value Fund, Goldman Sachs Money Market Fund, SSgA S&P 500 Index Fund, Vanguard Total Stock Market Index Fund, Commerce Short Term Government Bond Fund, AIM Funds Group Small Cap Growth “A” Fund, American Century Equity Income Advisor Class Fund and Vanguard Small Cap Value Index Fund.

6


Table of Contents

    In July 2004, with the change in custodian, the Company added the Fidelity Equity Income II Fund, Fidelity Diversified International Fund, Fidelity Mid Cap Stock Fund, Fidelity Freedom Income Fund, Fidelity Freedom 2010 Fund, Fidelity Freedom 2020 Fund, Fidelity Freedom 2030 Fund, Fidelity Freedom 2040 Fund, Fidelity Retirement Money Market Fund, and Spartan US Equity Index Fund. As part of this transition, the Goldman Sachs Money Market Fund and SSgA S&P 500 Index Fund were no longer offered as investment options. During 2006 the Fidelity Freedom 2005 Fund, Fidelity Freedom 2015 Fund, Fidelity Freedom 2025 Fund, Fidelity Freedom 2035 Fund, Fidelity Freedom 2045 Fund, and Fidelity Freedom 2050 Fund were added to the Plan’s investment options.
 
    Participants may roll over funds into the Plan from any qualified plan, subject to the approval of the plan administrator. Rollover contributions earn investment income and share in investment gains or losses. Participants are 100% vested in rollover contributions. Participants direct the investment of their contributions to any of the various investment options offered by the Plan.
 
    Assets of the Company Stock Fund include Commerce Bancshares, Inc. common stock. As a result, cash dividends on Commerce Bancshares, Inc. common stock are paid directly to the Company Stock Fund and allocated to the participants. Participants with balances in the Company Stock Fund have the option to reinvest their cash dividends in the Company Stock Fund or have dividends paid to them directly.
 
    Participant Accounts
 
    Each participant’s account is credited with the participant’s contribution, the Company’s matching and discretionary contributions, and an allocation of Plan earnings. The earnings allocation is based on the performance of the participant’s allocated investment fund balances. The benefit to which a participant is entitled is the vested portion of the participant’s account.
 
    Participants may make transfers between existing fund balances once during each calendar month. Participating employees may change future investment elections at any time upon notification to the Plan. Both transactions are done in 1% increments.
 
    Participant Vesting
 
    Participants are vested immediately in their contributions plus actual earnings thereon, however, only upon termination of employment are participants entitled to receive their contributions and accumulated earnings thereon. Company matching contributions and Company discretionary contributions are subject to the following vesting schedule:
         
Years of   Percentage
Vesting Service   Vested
Less than 3
    0 %
3 or more
    100 %

7


Table of Contents

    The following schedule is applicable to participant’s after-tax employer matching contributions and ESOP balances:
         
Years of   Percentage
Vesting Service   Vested
Less than 3
    0 %
3, but less than 4
    20 %
4, but less than 5
    40 %
5, but less than 6
    60 %
6, but less than 7
    80 %
7 or more
    100 %
    A participant will become fully vested in the value of all Company contributions in the event of death, permanent and total disability, or retirement on or after age 65, regardless of the participant’s years of vesting service. A year of vesting service generally is each Plan year during which the participant earns at least 1,000 hours of service and is over the age of 18.
 
    Forfeitures
 
    Forfeitures are based on the nonvested portion of the Company contribution upon employee termination. Forfeited amounts are applied as a reduction of contributions by the Company or by participating subsidiaries. Forfeitures were used to reduce the Company contribution by $281,766 in 2006, $106,200 in 2005 and $116,408 in 2004. The balance of unallocated forfeitures available to offset future Company contributions amounted to $10,039 and $9,741 at December 31, 2006 and 2005, respectively. At December 31, 2005, it was determined that $28,165 excess forfeitures had been withheld from certain employees terminating in 2005 and those forfeitures had been used to lower Company contributions. Corrections were made to the impacted participants in early 2006.
 
    Participant Loans
 
    A participant may borrow from the Plan amounts collateralized by the vested portion of his or her Plan account. These loans may not exceed the lesser of $50,000 or 50% of the participant’s vested account balance (excluding employee stock ownership plan account balances). The loans are repaid through payroll deductions over terms which are based upon the amounts borrowed and normally do not exceed five years and are secured by the balance in the participant’s account. Interest rates charged on participant loans are based on the Commerce Prime plus 1% at the date of the distribution and are fixed throughout the life of the loan. The participant may continue to make contributions to the Plan throughout the term of the loan.
 
    Administrative Expenses
 
    Certain administrative functions are performed by officers or employees of Commerce Bancshares, Inc. (the Company). No such officer or employee receives compensation from the Plan. Administrative expenses incident to the administration of the Plan may be paid by the Company and, if not paid by the Company, shall be paid by the Plan. A setup fee for new loans (currently $50) is deducted from the respective participant’s account. The Company elected to pay all other administration fees for the year ended December 31, 2006, 2005 and 2004 and presently intends to continue to do so, although the Company can, at its discretion, discontinue this practice.

8


Table of Contents

    Distributions
 
    Distributions of vested account balances are available upon termination, retirement, death or permanent and total disability. Distributions are made in lump sum amounts to the participant or designated beneficiaries.
 
(2)   Summary of Significant Accounting Policies
 
    Basis of Presentation
 
    The accompanying financial statements have been prepared on the accrual basis in conformity with accounting principles generally accepted in the United States of America.
 
    Investment Valuation
 
    The Plan’s investments are held in an account at Fidelity Investments. On each valuation date, as defined by the Plan, securities held by the Plan are valued at fair value and the increase or decrease in the value of securities held, plus any net income or loss of the Plan, is allocated to the participant’s accounts. Fair value of the mutual funds is based on quoted market prices from national securities exchanges. Shares of the Company Stock Fund are based upon the fair values of the underlying investments, which include Company stock and cash equivalents. Loans to participants are valued at amortized cost, which approximates fair value.
 
    Net appreciation (depreciation) in fair value of investments includes realized and unrealized gains and losses. Also included is the reinvestment of interest and dividends earned on funds invested in the mutual and Company Stock funds. Purchases and sales of securities are recorded on a trade-date basis (the date the order to buy or sell is executed). Interest is accrued as earned and dividend income is recorded on the ex-dividend date.
 
    Use of Estimates
 
    The Plan utilizes a number of informed estimates and assumptions relating to the reporting of assets and liabilities and the disclosure of contingent assets and liabilities to prepare these financial statements in conformity with U.S. generally accepted accounting principles. Actual results could differ from those estimates.
 
    Payment of Benefits
 
    Distributions to the participants of the Plan are recorded when paid.
 
(3)   Risks and Uncertainties
 
    The Plan invests in various investment securities. Investment securities are exposed to various risks, such as interest rate, 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.

9


Table of Contents

 
(4)   Company Stock Fund
    The Company Stock Fund is accounted for on a unitized accounting basis. The fund has a cash reserve in order to provide the liquidity necessary to process daily fund transactions by the close of market each business day. The cash reserve generally represents between one and five percent of the total fund value, and varies depending upon account activity. The reserve may consist of cash or cash equivalents. As of December 31, 2006 and 2005, the cash reserve totaled approximately $4.5 million and $5.1 million, respectively.
 
    In January 1995, all assets held by the Company’s qualified employee stock ownership plan were merged into the Plan and remain under a portion of the Plan that qualifies as an employee stock ownership plan (ESOP). All Company common stock attributable to the ESOP has been fully allocated to participant account balances at December 31, 2006 and 2005 and is held as units of the Company Stock Fund. At December 31, 2006, 983 participants had an ESOP related account balance.
 
    Information about changes in ESOP assets included in the Company Stock Fund for the years ended December 31, 2006, 2005 and 2004, is as follows:
                         
    2006     2005     2004  
Beginning balance:
  $ 32,769,035     $ 34,238,150     $ 35,591,151  
Unrealized appreciation (depreciation) (including reinvested dividends and interest)
    (1,536,167 )     754,694       2,192,447  
Benefits paid to participants
    (1,076,924 )     (1,868,561 )     (2,323,985 )
Transfers to participant- directed investments
    (142,328 )     (355,248 )     (1,221,463 )
 
                 
Ending balance
  $ 30,013,616     $ 32,769,035     $ 34,238,150  
 
                 
    In addition, the Company Stock Fund utilizes available cash from participant and employer directed contributions and dividends to purchase Commerce Bancshares Inc. common stock on the open market. During 2006, 2005 and 2004 total dividends paid on shares of Company stock held by the Company Stock Fund and the amount thereof which was distributed directly to the participants is as follows:
                         
    2006   2005   2004
Dividends paid on shares of Company stock
  $ 3,054,000     $ 2,925,000     $ 2,842,000  
Portion of dividend distributed to participants
    2,004,000       1,998,000       2,021,000  

10


Table of Contents

(5)   Investments
 
    The following table sets forth investments that represent 5% or more of the market value of the Plan’s net assets at December 31, 2006 or 2005:
                 
    2006   2005
Commerce Bancshares, Inc. Common Stock Fund:
               
Commerce Bancshares, Inc. common stock
  $ 157,562,381     $ 165,705,549  
Fidelity Retirement Money Market Fund
    4,515,875       5,147,912  
Fidelity Retirement Money Market Fund
    27,907,348       22,678,824  
Spartan US Equity Index Fund
    20,059,737       17,684,975  
Commerce Growth Fund
    20,805,698       19,384,432  
    During 2006, 2005 and 2004 the Plan’s investments appreciated (depreciated) in value as follows:
                         
    2006     2005     2004  
Commerce Bancshares, Inc.
                       
Common Stock Fund
  $ (3,782,228 )   $ 13,531,897     $ 11,456,810  
Mutual Funds
    9,910,773       2,862,903       5,015,504  
 
                 
 
  $ 6,128,545     $ 16,394,800     $ 16,472,314  
 
                 
(6)   Federal Income Taxes
 
    In a determination letter dated July 11, 2002, the Internal Revenue Service stated that the Plan, as amended through August 16, 2001, met the requirements of section 401(a) of the Internal Revenue Code (IRC) and the Trust established thereunder was exempt from federal tax under section 501(a) of the IRC. Although the Plan has been amended since receiving the determination letter, the plan administrator believes that the Plan, as designed and operated, is in compliance with the applicable provisions of the IRC.
 
    The Company is entitled to deduct for federal income tax purposes the amount of contributions made by the Company and each of its participating subsidiaries for the benefit of employees. In general, neither such contributions nor the income from the trust will be taxable to participants as income prior to the time such participants receive a distribution from the Plan. Participant contributions are not required to be included in the employees’ taxable income until the year or years in which they are distributed or made available to them.
 
(7)   Transactions with Related Parties
 
    Certain Plan investments are shares of mutual funds managed by The Commerce Trust Company, a division of Commerce Bank, N.A. The Company Stock Fund also includes shares of Company common stock; therefore, these transactions qualify as party-in-interest transactions. Plan investments also include shares of mutual funds managed by Fidelity Investments, the custodian and record keeper of the Plan. These are exempt party-in-interest transactions under ERISA.

11


Table of Contents

 
    Transactions with the Company and its affiliates during the years ended December 31, 2006, 2005, and 2004 were as follows:
                                         
    Purchases   Sales
                                    Realized
    Units   Cost   Units   Proceeds   Gains (Losses)
2006:
                                       
Company Stock Fund
    695,599     $ 14,574,316       931,658     $ 19,567,293     $ 7,881,426  
Commerce Mutual Funds
    639,380       13,864,603       571,956       11,633,230       272,720  
 
                                       
2005:
                                       
Company Stock Fund
    854,335     $ 17,256,639       1,169,790     $ 23,258,225     $ 7,064,064  
Commerce Mutual Funds
    638,958       13,345,575       845,816       17,364,629       (735,870 )
 
                                       
2004:
                                       
Company Stock Fund
    726,590     $ 13,034,889       1,351,172     $ 24,313,647     $ 9,723,831  
Commerce Mutual Funds
    678,205       13,657,037       745,589       15,162,790       (1,349,861 )
(8)   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 the provisions of ERISA. In the event of Plan termination, participants would become 100% vested in their employer contributions.
 
(9)   Plan Amendment
 
    During 2006, the Plan was amended as follows:
    Dividends paid on Commerce Bancshares, Inc. common stock will be automatically reinvested into each participant’s stock account, unless the participant makes an affirmative election to receive payment of the dividends directly. The Plan was also amended to provide that a terminated participant’s non-vested account balance will be forfeited upon the earlier of the date the participant receives distribution of his vested balance, or the occurrence of a 5-year break in service.
 
    Employees that are acquired through an acquisition will be eligible to participate in the Plan on the entry date that coincides with the effective date of the acquisition regardless of whether they meet the requirements for participation. Years of eligibility service will include all years of service with the acquired company. Acquired employees will be 100% vested in all accounts under the Plan effective as of the effective date of the acquisition.
 
    A terminated participant’s non-vested account balance will be forfeited upon the earlier of the date the participant receives distribution of his vested balance, or the occurrence of a 5-year break in service.
    During 2005 the Plan was amended as follows:
    Company matching percentage was changed to a graded matching percentage from 50% —100% determined by age plus years of employment on the first 7% of eligible compensation.
 
    Company is allowed to make a discretionary contribution. In addition, the Company may specify different rates of discretionary contributions for different groups of participants.

12


Table of Contents

    Automatic rollover of amounts from $1,000 to $5,000 to an IRA designated by the Administrator without participant consent if the participant does not elect to have such distribution paid directly to an eligible retirement plan.
(10)   Subsequent Event
 
    Subsequent to December 31, 2006, the Plan was notified that it did not pass certain parts of the nondiscrimination testing. During May 2007, refunds were made to certain active participants to return to them excess deferral contributions and matching contributions of $151,841 and $33,384, respectively, as required to satisfy the relevant nondiscrimination provisions of the Plan.

13


Table of Contents

Schedule 1
COMMERCE BANCSHARES PARTICIPATING INVESTMENT PLAN
Schedule H, line 4i — Schedule of Assets (Held at End of Year)
December 31, 2006
                         
    Number              
Identity of issue   of shares     Cost   Fair Value  
Commerce Bancshares, Inc. Common Stock Fund:*
                       
Commerce Bancshares, Inc. Common Stock*
    3,251,246     $ 92,291,802   $ 157,562,381  
Fidelity Retirement Money Market Fund
    4,515,875     4,515,875     4,515,875  
 
                 
Total Common Stock Fund
    7,718,013       96,807,677     162,078,256  
 
                     
 
                       
Mutual Funds
                       
Commerce Asset Allocation Fund*
    393,172       * *     7,647,194  
Commerce Bond Fund*
    632,214       * *     11,405,140  
Commerce Growth Fund*
    802,379       * *     20,805,698  
Commerce International Equity Fund*
    125,285       * *     3,484,170  
Commerce MidCap Fund*
    178,427       * *     6,136,115  
Commerce Short Term Government Bond Fund*
    124,764       * *     2,185,872  
Commerce Value Fund*
    182,599       * *     5,140,168  
AIM Funds Group Small Cap Growth “A” Fund
    83,349       * *     2,436,280  
American Century Equity Income Advisor Class Fund
    900,033       * *     7,722,287  
Fidelity Diversified International Fund*
    256,506       * *     9,477,879  
Fidelity Equity Income II Fund*
    91,917       * *     2,228,065  
Fidelity Freedom 2010 Fund*
    127,957       * *     1,870,726  
Fidelity Freedom 2020 Fund*
    123,672       * *     1,920,629  
Fidelity Freedom 2030 Fund*
    56,393       * *     903,983  
Fidelity Freedom 2040 Fund*
    94,315       * *     894,110  
Fidelity Freedom Income Fund*
    49,111       * *     566,739  
Fidelity Mid Cap Stock Fund*
    173,311       * *     5,050,275  
Fidelity Retirement Money Market Fund*
    27,907,348       * *     27,907,348  
Spartan US Equity Index Fund
    399,756       * *     20,059,737  
Vanguard Small Cap Value Index Fund
    319,376       * *     5,445,352  
Vanguard Total Stock Market Index Fund
    364,260       * *     12,417,619  
 
                     
Total Mutual Funds
                    155,705,386  
 
                     
 
                       
Loans to Participants—Interest rates on these loans range from 5.00% to 10.50%
                    6,709,893  
 
                     
 
                       
Total assets held for investment purposes
                  $ 324,493,535  
 
                     
 
*   Related party
 
**   In accordance with instructions to the Form 5500, the Plan is no longer required to disclose the cost component of participant-directed investments.

14


Table of Contents

Schedule 2
COMMERCE BANCSHARES PARTICIPATING INVESTMENT PLAN
Schedule H, line 4j — Schedule of Reportable Transactions
Year ended December 31, 2006
                                                         
                                            Current    
                            Expense           value of    
                            incurred   Cost   asset on    
    Purchase   Selling   Lease   with   of   transaction   Gain
    price   price   rental   transaction   asset   date   (loss)
Commerce Bancshares, Inc.
                                                       
Common Stock Fund*
  $ 14,574,316                         14,574,316       14,574,316        
Commerce Bancshares, Inc.
                                                       
Common Stock Fund*
  $       19,567,293                   13,096,493       19,567,293       6,470,800  
 
*   Related party

15


Table of Contents

EXHIBIT INDEX
23.1   Consent of Independent Registered Public Accounting Firm
 
23.2   Consent of Independent Registered Public Accounting Firm