UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 ------------------------ FORM 11-K ----------------------- (Mark One) [ X ] Annual Report Pursuant to Section 15(d) of the Securities Exchange Act of 1934 For the fiscal year ended December 31, 2006 OR [ ] Transition Report Pursuant to Section 15(d) of the Securities Exchange Act of 1934 For the transition period from ____________ to ________________ Commission File Number 33-26115 A. Full title of the plan and the address of the plan, if different from that of the issuer named below: PATRIOT TRANSPORTATION HOLDING, INC. PROFIT SHARING AND DEFERRED EARNINGS PLAN B. Name of issuer of the securities held pursuant to the plan and the address of its principal executive office: Patriot Transportation Holding, Inc. 1801 Art Museum Drive Jacksonville, Florida 32207 - ----------------------------------------------------------------- Patriot Transportation Holding, Inc. Profit Sharing and Deferred Earnings Plan Index Page(s) Reports of Independent Registered Certified Public Accounting firms..2-3 Financial Statements Statements of Net Assets Available for Benefits December 31, 2006 and 2005............................................4 Statement of Changes in Net Assets Available for Benefits Year Ended December 31, 2006..........................................5 Notes to Financial Statements.......................................6-10 Supplemental Schedule Schedule H, Line 4i - Schedule of Assets (Held at End of Year) December 31, 2006 ...................................................11 Note: Other schedules required by 29 CFR 2520.103-10 of the Department of Labor's Rules and Regulations for Reporting and Disclosure under ERISA have been omitted because they are not applicable, or are not required for participant directed investment transactions. Report of Independent Registered Certified Public Accounting Firm To the Participants and Administrator of Patriot Transportation Holding, Inc. Profit Sharing and Deferred Earnings Plan We have audited the accompanying statement of net assets available for benefits of the Patriot Transportation Holding, Inc. Profit Sharing and Deferred Earnings Plan (the Plan) as of December 31, 2006, 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 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. We were not engaged to perform an audit of the Plan's internal control over financial reporting. Our audit included consideration of internal control over financial reporting as a basis of designing audit procedures that are appropriate in the circumstances, but not for expressing an opinion on the effectiveness of the Plan's internal control over financial reporting. Accordingly, we express no such opinion. 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 audit provides 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 at December 31, 2006, 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. Our audit was performed for the purpose of forming an opinion on the financial statements taken as a whole. The accompanying supplemental schedule of assets (held at end of year) as of December 31, 2006 is presented for purposes of additional analysis and is not a required part of the financial statements but is 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. This 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 financial statements and, in our opinion, is fairly stated in all material respects in relation to the financial statements taken as a whole. /s/ Hancock Askew & Co LLP _____________________________ Hancock Askew & Co LLP Savannah, Georgia June 6, 2007 				2 Report of Independent Certified Public Accountants To the Participants and Administrator of Patriot Transportation Holding, Inc. Profit Sharing and Deferred Earnings Plan In our opinion, the accompanying statement of net assets available for benefits presents fairly, in all material respects, the net assets available for benefits of Patriot Transportation Holding, Inc. Profit Sharing and Deferred Earnings Plan (the "Plan") at December 31, 2005 in conformity with accounting principles generally accepted in the United States of America. 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 of this statement 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 statement is free of material misstatement. An audit includes examining, on a test basis, evidence supporting the amounts and disclosures in the financial statement, assessing the accounting principles used and significant estimates made by management, and evaluating the overall financial statement presentation. We believe that our audit provides a reasonable basis for our opinion. /s/ PricewaterhouseCoopers LLP ______________________________ PricewaterhouseCoopers LLP June 23, 2006 Jacksonville, Florida 				3 Patriot Transportation Holding, Inc. Profit Sharing and Deferred Earnings Plan Statements of Net Assets Available for Benefits December 31, 2006 and 2005 - ------------------------------------------------------------------ 				 2006 2005 ---- ---- Assets Investments, at fair value Investments $ 24,497,728 $ 22,128,560 Participant loans 1,363,947 1,194,552 ---------- ----------- Total investments 25,861,675 23,323,112 ---------- ----------- Contributions receivable Employer 13,504 12,244 Employee 31,586 28,673 ---------- ----------- Total contributions receivable 45,090 40,917 ---------- ----------- Total assets 25,906,765 23,364,029 ---------- ----------- Liabilities Excess contributions payable - 6,690 ---------- ----------- Total liabilities - 6,690 ---------- ----------- Net assets available for benefits $ 25,906,765 $ 23,357,339 ----------- ----------- 				4 Patriot Transportation Holding, Inc. Profit Sharing and Deferred Earnings Plan Statement of Changes in Net Assets Available for Benefits Year Ended December 31, 2006 - ---------------------------------------------------------------- 						 Additions to net assets attributed to Investment income Dividend and interest income $ 826,257 Net appreciation in fair value of investments 860,901 Other income-loan interest 83,788 ----------- Total investment income 1,770,946 ----------- Contributions Employer 793,717 Employee 1,852,662 Rollovers 137,541 ----------- Total contributions 2,783,920 ----------- Total additions 4,554,866 ----------- Deductions from net assets attributed to Distributions to participants 2,005,348 Administrative expenses 92 ----------- Total deductions 2,005,440 ----------- Net increase 2,549,426 ----------- Net assets available for benefits Beginning of year 23,357,339 ----------- End of year $ 25,906,765 ----------- 				5 Patriot Transportation Holding, Inc. Profit Sharing and Deferred Earnings Plan Notes to Financial Statements December 31, 2006 and 2005 - ---------------------------------------------------------------- 1. Description of the Plan The following description of Patriot Transportation Holding, Inc. (the "Company") Profit Sharing and Deferred Earnings Plan (the "Plan") provides only general information. Participants should refer to the Plan agreement for a more complete description of the Plan's provisions. General The Plan is a defined contribution plan available to all employees of the Company. The Plan is subject to the provisions of the Employee Retirement Income Security Act of 1974 (ERISA). Contributions Each year, participants may contribute up to 100% of pretaxannual compensation, as defined in the Plan. Participants may also contribute amounts representing distributions from other qualifieddefined benefit, defined contribution or other qualifiedplans, the Company matches 50% of the first 6% of the participant'sdeferred earnings contributions. The Company may make adiscretionary contribution to the Plan each year in an amountdetermined by the Board of Directors of the Company subjectto certain limitations relating to the aggregate compensation of participants. No discretionary contributions were made by the Company for the 2005 or 2006 Plan years. Participant Accounts Each participant's account is credited with the participant's contributions, the employer's matching contribution, an allocation of the employer's discretionary contributions and Plan earnings. The benefit to which a participant is entitled is the benefit that is available in the participant's vested account. Participants direct the investment of their contributions into various investment options offered by the Plan. The Plan currently offers a moneymarket fund, common/collective trust, mutual funds, Company stock and Florida Rock Industries, Inc. stock as investment options for participants. All participants who have not made an election are deemed to have elected to have contributions made to their accounts invested in the SunTrust Retirement Stable Asset Fund. Vesting Participants are fully vested in their voluntary contributions plus actual earnings thereon. If participants are employed on or after their retirement age, the company's matching and discretionary contributions are fully vested. In the event of termination by retirement, death or disability of the participant, 100% of the employer contributions will be distributed to the participant or the participant's designated beneficiary. 				6 Patriot Transportation Holding, Inc. Profit Sharing and Deferred Earnings Plan Notes to Financial Statements December 31, 2006 and 2005 - ------------------------------------------------------------------- Vesting (cont.) Vesting in the Company's matching and discretionary contributions plus actual earnings thereon is determined under the following schedules based on years of service. Matching Contributions 	 				 Vested Years of Service Percentage Less than 1 0% 1 20% 2 40% 3 60% 4 80% 5 100% Profit Sharing Contributions Vested Years of Service Percentage Less than 3 0% 3 20% 4 40% 5 60% 6 80% 7 100% Payment of Benefits On termination of employment, death or disability of a participant, benefits for distribution shall be determined based upon the participant's vested account balance on the date of distribution, which shall be made as soon as administratively feasible or later if so elected by the participant in amounts as provided in the Plan. Forfeited Accounts The non-vested portion of a terminated participant's account shall be forfeited and reallocated to the accounts of the remaining participants in the same manner as employer contributions were originally allocated to such participants. Any forfeiture from an employer discretionary account shall be allocated in the plan year in which the forfeiture occurs. Any forfeiture from an employer matching account shall be reallocated in the immediately following plan. Unallocated forfeitures totaled $195,860 and $96,896 at December 31, 2006 and 2005, respectively. Participant Loans Participants may borrow from their accounts a minimum of $1,000 and a maximum equal to the lesser of $50,000 or 50% of their vested account balance. Loans bear interest at the prevailing rate used by commercial lending institutions. Participants may have only two loans outstanding at any time. Loans are secured by the participant's remaining vested account balance. Loans terms are limited to five years except residential loans, which are payable up to 15 years. Loan repayment will be deducted from the participant's payroll over the term of the loan. Upon termination of employment with the Company, the outstanding balance of the loan, including accrued interest, is due immediately. 				7 Patriot Transportation Holding, Inc. Profit Sharing and Deferred Earnings Plan Notes to Financial Statements December 31, 2006 and 2005 - ----------------------------------------------------------------------- 2. Summary of Significant Accounting Policies Basis of Accounting The financial statements of the Plan are prepared under the accrual method of accounting in conformity with accounting principles generally accepted in the United States of America. Investments Valuation and Income Recognition Investments in the common stock ofthe Company and of Florida Rock Industries, Inc. are stated atfair value based upon quoted market prices at year-end. Unitsor shares of mutual funds and common/collective trusts arevalued at the net asset value of shares held by the Plan at year-end. Loans to participants are recorded at the unpaid balance ofthe individual loans as of year- end, which approximate fair value. The Plan presents in the statementof changes in net assets available for benefits the net appreciationor depreciation in fair value of investments which consists of therealized gains or losses and the unrealized appreciation or depreciation on these investments. Purchases and sales of securities are recorded on a trade-date basis. Interest income is recorded on the accrual basis when it is earned. Dividends are recorded on the basis of the ex-dividend date. Use of Estimates The preparation of financial statements in conformity with accounting principles generally accepted in the United States of America requires management to make significant estimates and assumptions that affect the reported amounts of assets andliabilities and changes therein, and disclosure of contingentassets and liabilities. Actual results could differ from thoseestimates. Benefit Payments Benefits are recorded when paid. Risks and Uncertainties The Plan provides for investment options in various investment securities. Investment securities are exposed to risks, such as interest rate, market risk and credit risk. Due to the level of risk associated with certain investment securities and the level of uncertainty related to changes in the value of investment securities, it is reasonably possible that changes in risks in the near term would materially affect participants' account balances and the amounts reported in the statement of net assets available for benefits and the statement of changes in net assets available for benefits. 				8 Patriot Transportation Holding, Inc. Profit Sharing and Deferred Earnings Plan Notes to Financial Statements December 31, 2006 and 2005 - --------------------------------------------------------------------- 3. Investments Investments which exceeded 5% or more of the Plan's net assets at December 31 are summarized as follows: - --------------------------------------------------------------------- 						 2006 2005 STI Classic Prime Quality Money Market Fund $ 7,036,042 $ 6,850,270 Florida Rock Industries Inc. common stock 3,306,107 3,211,967 T. Rowe Price Growth Stock Fund-R 2,546,424 2,556,906 Vanguard 500 Index Fund 2,162,239 2,070,631 Patriot Transportation Holding, Inc. common stock 1,409,231 * Participant loans 1,363,947 1,194,552 Longleaf Partners Fund 1,309,409 * - ----------------------------------------------------------------------- *Did not represent 5% or more of Plan's net assets at December 31, 2005. 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 as follows: 						 Common Stock $ 9,367 Mutual Funds 817,466 Common/collective trust 34,068 --------- Net appreciation in fair value of investments $ 860,901 ========= 4. Related Party Transactions Certain Plan investments are managed by SunTrust. SunTrust is the trustee as defined by the Plan and, therefore, these transactions qualify as party-in- interest transactions. Fees to the trustee are deducted from investment income. Certain administrative expenses are paid for by the Company without charge to the Plan. Such expenses amounted to $19,880 for the year ended December 31, 2006, and are not included in these financial statements. 5. Plan Termination While the Company has not expressed any intent to do so, it may terminate the Plan at any time. In the event of such termination, the accounts of all participants would become fully vested and the Company, by written notice to the Trustee and the Committee, may direct either complete distribution of the assets in the Trust Fund to the participants or, continue the Trust and the distribution of benefits at such time and in such manner as though the Plan had not been terminated. 6. Amendments The Plan was amended to adopt a new Plan document, the Defined Contribution Plan and Trust, a prototype plan, sponsored by SunTrust Bank, on September 18, 2006. This adoption did not significantly change any features of the Plan and did not retroactively eliminate any optional form of benefits that were available under the predecessor plan. 				9 Patriot Transportation Holding, Inc. Profit Sharing and Deferred Earnings Plan Notes to Financial Statements December 31, 2006 and 2005 7. Income Tax Status The Plan, prior to amendment as discussed in note 6, obtained its latest determination letter on May 14, 2004, in which the Internal Revenue Service stated that the Plan, as then designed, was in compliance with the applicable requirements of the Internal Revenue Code ("IRC"). The prototype Plan, adopted by the Company subsequent to the amendment as discussed in note 6, obtained its latest determination letter on August 26, 2002, in which the Internal Revenue Service stated that the prototype Plan, was in compliance with the applicable requirements of the Internal Revenue Code ("IRC"). The Plan administrator and the Plan's tax counsel believe that the Plan is currently designed and being operated in compliance with the applicable requirements of the IRC. 8. Financial Instruments Certain financial instruments potentially subject the Plan to concentrations of credit risk. These financial instruments consist of the SunTrust investment accounts, Company stock, Florida Rock Industries, Inc. stock and contributions receivable. The Plan limits its credit risk by maintaining its accounts with what the plan administrator believes to be high quality financial institutions. 9. Reconciliation of Financial Statements to Form 5500 The following is a reconciliation of net assets available for benefits per the financial statements at December 31, 2005 to Form 5500: 				 Net assets available for benefits per the financial statements $ 23,357,339 Excess contributions payable 6,690 ----------- Net assets available for benefits per the form 5500 $ 23,364,029 ----------- 				10 Patriot Transportation Holding, Inc. Profit Sharing and Deferred Earnings Plan Schedule H line 4i - Schedule of assets (held at end of year) December 31, 2006 			 					 Description of investment including maturity date, Identity of issue borrower rate of interest, Current or similar party collateral, par or value maturity date Cost ** - ----------------------------------------------------------------------------------- *STI Classic Prime Quality Money Market TSU-PMM Money Market $ 7,036,042 *Florida Rock Industries-Common Stock Common Stock 3,306,107 *Patriot Transportation Common Stock Common Stock 1,409,231 T. Rowe Price Growth Stock Fund-R Mutual Fund 2,546,424 Vanguard 500 Index fund Mutual Fund 2,162,239 T. Rowe Price Capital Appreciation Mutual Fund 808,997 Longleaf Partners Fund Mutual Fund 1,309,409 * STI Classic Life Vision Agg Grth I Mutual Fund 683,651 T. Rowe Price New Horizon Mutual Fund 788,299 *STI Classic Life Vision Moderate Grth I Mutual Fund 688,669 Chase Growth fund Mutual Fund 535,554 T. Rowe Price US Treasury Intermediate Mutual Fund 244,371 Mainstay Small Cap Opportunity Mutual Fund 409,685 Templeton Foreign Fund Mutual Fund 490,641 T. Rowe Price Equity Income Fund A Mutual Fund 259,448 *STI Classic Life Vision Conservative I Mutual Fund 169,602 MFS Research Bond Fund - A Mutual Fund 96,210 Fidelity Advisor Inflation Protected Bond Mutual Fund 49,772 Federated Mid Cap Index IS Mutual Fund 317,146 *SunTrust Retirement Stable Asset Fund Common/Collective Trust 1,186,231 --------- $ 24,497,728 *Participant loans Loans with interest ranging 1,363,947 from 4.0% to 10.5% -0- ----------- $ 25,861,675 ----------- * Party-in-interest as defined by ERISA ** Cost not required for participant-directed investments 				11 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 by the undersigned hereunto duly authorized. PATRIOT TRANSPORTATION HOLDING, INC., PROFIT SHARING AND DEFERRED EARNINGS PLAN By: /s/ Ray M. Van Landingham ------------------------------ Ray M. Van Landingham Vice President, Chief Financial Officer, and Secretary of Patriot Transportation Holding, Inc. (Principal Financial Officer) 				12 EXHIBIT 23.1 CONSENT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM We consent to the incorporation by reference in the Registration Statement (Form S-8 No. 333-62676) pertaining to the Patriot Transportation Holding, Inc. Profit Sharing and Deferred Earnings Plan of our report dated June 6, 2007, with respect to the financial statements and supplemental schedule of the Patriot Transportation Holding, Inc. Profit Sharing and Deferred Earnings Plan included in this Annual Report (Form 11-K) for the year ended December 31, 2006. /s/ Hancock Askew & Co LLP __________________________ Hancock Askew & Co LLP June 26, 2007 				13 EXHIBIT 23.1 Consent of Independent Registered Certified Public Accounting Firm We hereby consent to the incorporation by reference in the Registration Statement on Form S-8 (No. 333-125099) of Patriot Transportation Holding, Inc. of our report dated June 23, 2006 relating to the financial statements of Patriot Transportation Holding, Inc. Profit Sharing and Deferred Earnings Plan, which appears in this Form 11-K. /s/ Pricewaterhousecoopers LLP _________________________________ PricewaterhouseCoopers LLP Jacksonville, Florida June 26, 2007 				14