The following discussion should be read in conjunction with our consolidated financial statements and notes thereto which appear elsewhere in this Annual Report on Form 10-K. The following discussion contains forward-looking statements and should also be read in conjunction with the "Cautionary Statement" included at the beginning of this Annual Report on Form 10-K.

Overview American Science and Engineering, Inc. develops and manufactures state-of-the-art X-ray inspection systems for homeland security, force protection, and other critical defense applications. We provide maintenance, warranty, engineering, and training services related to these products.

Our primary technologies are Z Backscatter technology which is used to detect explosives, illegal drugs, and other contraband even when artfully concealed in complex backgrounds; and other technologies that expand the detection capability of our products beyond the material discrimination features of the Z Backscatter technology to include the penetration capability of high-energy transmission X-rays for dense cargos and/or other detection techniques, such as radioactive threat detection.

Net sales and contract revenues for fiscal 2012 decreased by 27% to $203,552,000 compared to fiscal 2011 revenues of $278,576,000. We reported income before taxes of $32,458,000 in fiscal 2012 compared to an income before taxes of $64,875,000 in the previous fiscal year. Net income for fiscal 2012 was $21,422,000 ($2.34 per share, on a diluted basis) as compared to a net income of $42,817,000 ($4.63 per share, on a diluted basis) in fiscal 2011. Backlog at March 31, 2012 was $192,571,000, an 11% decrease from the year-end backlog of $215,228,000 reported at March 31, 2011.

2012 Compared to 2011

Results of Operations Total net sales and contract revenues of $203,552,000 in fiscal 2012 decreased by $75,024,000 or 27% from the previous year. Revenues related to product sales and contracts decreased by $78,694,000 or 41% due to the factors described further below. Z Backscatter system revenues decreased by $53,356,000, due to a decrease in number of units sold during the year attributable to the force reduction in the Middle East and unrest due to the Arab Spring uprisings delaying procurements in other areas of the world. Cargo Inspection System revenues decreased by $29,768,000 as compared to the prior year due to lower demand, and a fewer number of systems under construction as compared to the prior year. Contract research and development (CRAD) revenues decreased by $411,000, due in part to the termination for convenience of one of the CRAD contracts during fiscal 2012. These revenue decreases were offset by an increase of $2,833,000 in Parcel Inspection system sales from the prior year attributable primarily to one large multi-system order received in fiscal 2011 and fulfilled in fiscal 2011 and fiscal 2012 and an increase in aftermarket sales of $2,007,000 due to increased spares parts volume during the year. Service revenues increased in fiscal 2012 by $3,670,000 or 4% to $89,428,000, due primarily to service contracts entered into in the current year on the increased installed base.

In fiscal 2012 and fiscal 2011, 66% and 68% of our revenues, respectively, were from domestic customers (as determined based upon the customer's country of domicile). In fiscal 2012, we had revenue from one customer which accounted for 23% of total sales. In fiscal 2011, we had revenue from three customers which accounted for 53% of total sales.

Cost of sales and contracts of $110,435,000 in fiscal 2012 decreased by $38,939,000 or 26% from the previous year. Cost of product sales and contracts of $65,500,000 in fiscal 2012 decreased by $38,562,000 or 37% as compared to the prior year. Cost of product sales and contracts totaled 57% of revenues in fiscal 2012, as compared to 54% of revenues in fiscal 2011. The resultant decrease in gross margin is primarily the result of loss accruals provided for during the year on certain long-term contracts, the write-down of certain equipment to a lower of cost or net realizable value, and inventory reserves accrued for during the period for excess and obsolete inventory. The cost of service revenues decreased $377,000 or 1% from the prior year. Cost of service revenues totaled 50% of revenues in fiscal 2012 as compared to 53% of revenues in fiscal 2011. The resultant improvement in gross margin is due primarily to decreased material and third party service costs for equipment under fixed price service contracts as compared to the prior year.

Selling, general and administrative expenses in fiscal 2012 decreased by $6,515,000 to $35,624,000 as compared to $42,139,000 in fiscal 2011 and represented 17.5% of revenues in fiscal 2012 as compared to 15% of revenues in fiscal 2011. The decrease in selling, general and administrative expenses over the prior period was primarily the result of: a decrease in incentive compensation of $6,244,000 as certain incentive compensation goals were not achieved in the current year; a decrease in legal fees of $859,000 from the prior year as fiscal 2011 contained expenses related to due diligence activities on a potential acquisition that was later abandoned; and a decrease in marketing costs of $597,000 related primarily to reduced trade show, conference, and demonstration related costs. These expense decreases were offset in part by an increase in payroll and payroll related costs of $1,023,000 attributable to increased headcount

Company-funded research and development spending increased by $2,925,000 to $25,544,000 in fiscal 2012 which is a 13% increase as compared to the $22,619,000 spent in fiscal 2011. Research and development spending represented 13% of revenues in fiscal 2012 as compared to 8% of revenues in fiscal 2011. Research and development spending increased from the prior year and the Company continued its commitment to new product development, the development of new applications and new technologies, and design modifications and enhancements to its existing products.

Other income was $509,000 in income in fiscal 2012 as compared to $431,000 in income in fiscal 2011.

We reported pre-tax income of $32,458,000 in fiscal 2012 as compared to a pre-tax income of $64,875,000 in the previous fiscal year primarily due to the items noted above. We recorded income tax expense of $11,036,000 in fiscal 2012 as compared to $22,058,000 in the prior fiscal year. Our effective tax rate was 34.0% in both fiscal 2012 and in fiscal 2011.

We reported net income of $21,422,000 in fiscal 2012 as compared to net income of $42,817,000 in fiscal 2011.

2011 Compared to 2010

Results of Operations Total net sales and contract revenues of $278,576,000 in fiscal 2011 increased by $36,483,000 or 15% from the previous year. Revenues related to product sales and contracts increased by $27,108,000 or 16% due to the following factors. Z Backscatter system revenues increased by $18,744,000, attributable to sales of both our ZBV Militarized Trailer system, which was introduced in fiscal 2009, and our Z Backscatter Van, which had an increase in number of units sold during the year to U.S. government and international customers. Parcel Inspection system sales increased by $7,520,000 from the prior year due to an increase in the number of units delivered in the current year. Cargo Inspection system revenues increased by $3,095,000 over the previous year as the volume of systems under construction and/or delivered increased over the previous year. Contract research and development (CRAD) revenues increased by $2,515,000, which was attributable primarily to two contracts worked during the year. These revenue increases were offset by a decrease in aftermarket sales of $4,764,000 due to a large spare parts order fulfilled in fiscal 2010 which was not repeated in fiscal 2011. Service revenues increased in fiscal 2011 by $9,375,000 or 12% to $85,758,000, due primarily to new service contracts entered into in the current year on the increased installed base.

In both fiscal 2011 and fiscal 2010, 68% of our revenues were from domestic (based upon the customer's country of domicile) customers. In fiscal 2011, we had sales to three customers which accounted for 53% of total sales. In fiscal 2010, we had sales to two customers which accounted for 36% of total sales.

Cost of sales and contracts of $149,374,000 in fiscal 2011 increased by $18,351,000 or 14% from the previous year. Cost of product sales and contracts of $104,062,000 in fiscal 2011 increased by $12,508,000 or 14% as compared to the prior year. Cost of product sales and contracts totaled 54% of revenues in fiscal 2011, as compared to 55% of revenues in fiscal 2010. This decrease in costs as a percentage of revenue is due primarily to an increase in shipments of higher margin Z Backscatter systems over the prior year and improved margins on both Cargo and Parcel Inspection systems as a result of increased volume. The cost of service revenues increased $5,843,000 or 15% from the prior year. Cost of service revenues totaled 53% of revenues in fiscal 2011 as compared to 52% of revenues in fiscal 2010. This increase in costs as a percentage of revenue is due primarily to increased material and travel-related costs being incurred to service equipment under fixed price service contracts as compared to the prior year.

Selling, general and administrative expenses in fiscal 2011 increased by $5,157,000 to $42,139,000 as compared to fiscal 2010 and represented 15% of revenues in both fiscal 2011 and fiscal 2010. The increase in selling, general and administrative expenses over the prior period was primarily the result of:
1) an increase in payroll and payroll related costs of $2,430,000 attributable to increased headcount; 2) an increase in legal fees of $876,000 attributable primarily to due diligence activities on a potential acquisition that was abandoned earlier in the year and other routine business activities; 3) an increase in incentive compensation costs of $761,000 as we achieved certain incentive compensation goals in the current year; 4) an increase in travel expenses of $644,000 related to sales and marketing related efforts; and 5) an increase in marketing costs of $456,000 related primarily to trade show and demonstration related costs.

Company-funded research and development spending increased by $2,855,000 to $22,619,000 in fiscal 2011 which is a 14% increase as compared to the $19,764,000 spent in fiscal 2010. Research and development spending represented 8% of revenues in both fiscal 2011 and fiscal 2010. The fiscal 2011 research and development efforts were focused on new product development, new technologies, the development of new applications, and design modifications and enhancements to existing products.

Other income was $431,000 in income in fiscal 2011 as compared to $522,000 in income in fiscal 2010.

We reported pre-tax income of $64,875,000 in fiscal 2011 as compared to a pre-tax income of $54,846,000 in the previous fiscal year primarily due to the items noted above. We recorded income tax expense of $22,058,000 in fiscal 2011 as compared to $18,670,000 in the prior fiscal year. Our effective tax rate was 34.0% in both fiscal 2011 and in fiscal 2010, as decreases in fiscal 2011 state income tax credits were offset by increased usage of manufacturing and research and development credits.

We reported net income of $42,817,000 in fiscal 2011 as compared to net income of $36,176,000 in fiscal 2010.

Liquidity and Capital Resources

Cash and cash equivalents at year-end decreased by $35,775,000 to $24,369,000 at March 31, 2012 as compared to $60,144,000 at March 31, 2011. In addition, we had $170,834,000 and $110,141,000 of short-term investments at March 31, 2012 and March 31, 2011, respectively.

Cash flow provided by operations of $51,019,000 resulted from the following:

† Reported net income of $21,422,000 adjusted for the following non-cash items:

† Depreciation and amortization of $5,768,000;

† Stock compensation expense of $1,799,000;

† Increases in deferred income taxes of $1,750,000;

† The amortization of bond premiums of $2,689,000; and

† The provision for contracts, inventory and accounts receivable reserves of $2,998,000.

† A decrease of $13,876,000 in unbilled costs and fees as billing milestones were reached on certain contracts which had significant unbilled balances at the end of fiscal 2011.

† A decrease of $11,819,000 in accounts receivable due primarily to lower revenues in the fourth quarter of fiscal 2012 as compared to the fourth quarter of fiscal 2011.

† An increase of $5,838,000 in customer deposits due to milestone payments received on certain contracts entered into in the current year.

These cash contributors were offset by:

† A decrease in accrued expenses of $4,530,000 due primarily to the payment of fiscal 2011 year-end bonuses during fiscal 2012. Incentive compensation accruals at the end of fiscal 2012 are comparatively lower than those in fiscal 2011 due to the lower financial results in fiscal 2012.

† An increase in inventories of $4,333,000 due primarily to an increase in finished goods due to the building of certain systems in anticipation of future demand.

† An increase of $3,609,000 in prepaid expenses and other assets due primarily to an increase in prepayments of estimated taxes in fiscal 2012 and an increase in prepayments to certain subcontractors for custom components purchased during the year.

Net cash of $68,552,000 was used for investing activities in fiscal 2012. We purchased $283,685,000 in short-term investments during the year, and had maturities of $220,293,000 on short-term investments. Net fiscal 2012 capital expenditures totaled $5,160,000 versus $5,301,000 for fiscal 2011. Investments in fixed assets were comprised primarily of information technology expenditures, leasehold improvements, and equipment used in production.

At March 31, 2012, short-term investments and cash equivalents were invested primarily in corporate debentures/bonds, commercial paper, government agency bonds, treasury bills, money market funds and certificates of deposit. Although management believes our investment policy is conservative in nature, certain short-term investments in commercial paper can be exposed to the credit risk of the underlying companies to which they relate and interest earned on these investments is subject to interest rate fluctuations. The weighted average days to maturity for investments held at March 31, 2012 was 194 days.

Net cash used for financing activities was $18,242,000 in fiscal 2012. We increased our quarterly dividend rate from $0.30 per quarter to $0.50 per quarter during the fiscal year resulting in a total of $14,423,000 in quarterly dividend payments for the year. We used $20,051,000 to repurchase 320,207 shares of common stock to complete our Stock Repurchase Program. During the year, our bank reduced our collateral requirement on outstanding letters of credit resulting in a $13,570,000 reduction in restricted stock required to collateralize outstanding standby letters of credit as compared to the prior year. In addition, we received proceeds of $4,287,000 from exercises of employee stock options.

We had in place in prior years a Loan and Security Agreement with Silicon Valley Bank which provided a $30.0 million facility to support routine letters of credit and working capital needs. The Loan and Security Agreement expired on November 12, 2010 and we decided not to renew this facility given the cash flows provided from operations and our available cash and investments balance. At the time of such decision, we had not drawn on this facility since June of 2002 and had used this credit facility exclusively to issue standby letters of credit.

Under the terms of this Loan and Security Agreement, we were required to pay certain one-time facility fees which were being amortized over the life of the facility and other unused credit fees. Total expenses incurred related to these fees were $94,000 and $227,000 in fiscal 2011 and 2010, respectively.

In the normal course of business, we may provide certain customers and potential customers with performance guarantees, which are generally backed by standby letters of credit. In general, we would only be liable for the amount of these guarantees in the event of default in the performance of its obligations, the probability of which is remote in management's opinion. At March 31, 2012, we had outstanding $29,981,000 in standby letters of credit. Upon expiration of our Loan and Security Agreement, these outstanding standby letters of credit became cash-secured at amounts ranging from 105% to 110% of the value of outstanding letters of credit. During the first quarter of fiscal 2012, the bank reduced this collateral requirement from 52% to 61% of the value of outstanding letters of credit. This collateral requirement resulted in a restricted cash balance of $15,890,000 at March 31, 2012, of which $4,183,000 was considered long-term restricted cash due to the expiration date of the underlying letters of credit.

As of March 31, 2012, $395,000 of our cash was held offshore, and while we do not currently believe there are any material limitations or restrictions on our ability to repatriate profits there may be tax consequence or changes in statutory rules which would affect our ability to do so.

In recent years, we have funded our operations and capital expenditures with cash generated by operations, including deposits from customers on long-term projects and from proceeds received from option exercises. We currently have no line of credit facility and believe that our cash flows from operations, and cash and investments on hand are sufficient to meet the current and foreseeable operating requirements of our business.

Contractual Obligations: We lease certain facilities under non-cancelable leases. In addition, in the normal course of business, we enter into purchase orders with our vendors for the purchase of materials or services to meet our production needs. The following table summarizes our contractual obligations as of March 31, 2012.

                                                               Payment due by period
                                                   Less than 1                                      After 5
(In thousands)                         Total           year          1-3 years      3-5 years        years
Recorded Contractual Obligations:
Lease financing liability            $   5,754    $        1,351    $     3,000    $     1,403               -
Other long-term obligations                 26                 9             17              -               -

Operating leases                         1,241               367            649            225               -
Purchase commitments                    24,059            14,598          9,461              -               -

Inflation: We do not believe that inflation has had a material effect on our results of operations in each of fiscal 2012, 2011 and 2010. There can be no assurance, however, that our business will not be affected by inflation in the future.

Off-Balance Sheet Arrangements: During the fiscal year ended March 31, 2012 we did not have any material off-balance sheet arrangements.

Critical Accounting Policies

We consider certain accounting policies related to revenue recognition, inventories and related allowances for obsolete and excess inventory, and income taxes to be critical policies due to the estimation processes involved in each.

Revenue Recognition: We recognize certain Cargo Inspection, Z Backscatter, Parcel and Personnel Screening System and after-market part sales, in accordance with Financial Accounting Standards Board Accounting Standards Codification ("FASB ASC") 605-10, Revenue Recognition, which requires that four basic criteria must be met before revenue can be recognized: (1) persuasive evidence of an arrangement exists; (2) delivery has occurred or services rendered;
(3) the fee is fixed and determinable; and (4) collectability is reasonably assured.

Infrequently, the Company receives requests from customers to hold product being purchased from us for a valid business purpose. We recognize revenue for such arrangements provided the transaction meets, at a minimum, the following criteria: a valid business purpose for the arrangement exists; risk of ownership of the purchased product has been transferred to the buyer; there is a fixed delivery date that is reasonable and consistent with the buyer's business purpose; the product is ready for shipment; the Company has no continuing performance obligation in regards to the product and the products have been

segregated from our inventories and cannot be used to fill other orders received. There were no products being held under these arrangements at March 31, 2012, March 31, 2011 or March 31, 2010.

Certain of our contracts are multiple-element arrangements, which include standard products, custom-built systems or contract engineering projects, services (such as training), and service and maintenance contracts. In accordance with FASB ASC 605-25, Revenue Recognition - Multiple Element Arrangements as amended by Accounting Standards Update No. 2009-13 adopted retroactively to April 1, 2009, revenue arrangements that include multiple elements are analyzed to determine whether the deliverables can be divided into separate units of accounting or treated as a single unit of accounting. The consideration we receive is allocated among the separate units of accounting based on their relative selling prices determined based on prices of these elements as sold on a stand-alone basis, and the applicable revenue recognition criteria are applied to each of the separate units. Generally, there is no customer right of return provision in the Company's sales agreements. Revenues are allocated to a delivered product or service when all of the following criteria are met: (1) the delivered item has value to the customer on a standalone basis; and (2) if the arrangement includes a general right of return relative to the delivered item, delivery or performance of the undelivered item is considered probable and substantially in our control.

Revenues for certain long-term, custom-built systems or contract engineering projects are recognized on a percentage of completion basis. The lengths of these contracts typically range from one to three years from order to delivery and acceptance. Percentages-of-completion are determined by relating the actual costs of work performed to date for each contract to our estimated final costs. Revisions in costs and profit estimates are reflected in the period in which the facts causing the revision become known.

We recognize sales for our systems that are produced in a standard manufacturing operation, have minimal customer site installation requirements and have shorter order to delivery cycles, when title passes and when other revenue recognition criteria are met. Management believes the customer's post-delivery acceptance provisions and installation requirements on certain of these systems are perfunctory and inconsequential and the costs of installation at the customer's site are accrued at the time of revenue recognition. We have demonstrated a history of customer acceptance subsequent to shipment and installation of these systems. For systems which entail more significant installation efforts and site work and/or have non-standard customer acceptance provisions, revenue recognition is deferred until installation is complete and customer acceptance has occurred.

Service revenues are recognized on time and materials engagements as the services are provided. Service contract revenues are recognized as service is performed over the length of the contract which reasonably approximates the period service revenues are earned.

Training and service contracts deliverables are accounted for separately from the delivered product elements as our undelivered products have value to our customers on a stand-alone basis. Accordingly, service revenue is deferred and recognized as such services are performed.

For all fixed price and long-term contracts, if a loss is anticipated on the contract, a provision is made in the period in which such losses are determined.

We record billed shipping and handling fees and billed out-of-pocket expenses as revenue and the associated costs as cost of goods sold in the accompanying consolidated statements of operations.

Certain contracts require payments from the customer upon execution of the agreement that are included in customer deposits. Individual customer deposits are reduced by the amount of revenue recognized on the contract until a zero balance is reached. Revenue recognized in excess of billings under the contracts is included in unbilled costs and fees in the accompanying balance sheet. Of the amounts in unbilled costs and fees at March 31, 2012, $3,119,000 (97%) is expected to be billed and collected during fiscal 2013.

Under the terms of certain of our cost reimbursement contracts, we are not permitted to bill customers a specified portion of the contract value until completion. Such retainages (approximately $87,000 and $76,000 at March 31, 2012 and March 31, 2011, respectively) result from both commercial contract retentions and government contract withholdings generally for up to 15% of fees, as well as the difference between the actual and provisional indirect cost billing rates. Retainages are included in the accompanying consolidated balance sheets as components of unbilled costs and fees. The accuracy and appropriateness of our direct and indirect costs and expenses under these cost reimbursement contracts and our accounts receivable recorded pursuant to such contracts, are subject to regulation and audit, including by the U.S. Defense Contract Audit Agency ("DCAA") or by other appropriate agencies of the U.S. government. Such agencies have the right to challenge the Company's cost estimates or allocations with respect to any government contract. Additionally, a portion of the payments to the Company under government contracts are provisional payments that are subject to potential adjustment upon audit by such agencies. Historically, such audits have not resulted in any significant disallowed costs. Although we can give no assurances, in the opinion of management, any adjustments likely to result from inquiries or audits of our contracts will not have a material adverse impact on our financial condition or results of operations.

Inventories and Related Allowance for Obsolete and Excess Inventory:
Inventories consist of material, labor and manufacturing overhead and are recorded at the lower of cost or net realizable value. Excessive manufacturing overhead costs such as idle facility expense, freight, handling costs and wasted material (spoilage) attributable to abnormally low volumes (levels that materially differ from budgeted production plans due primarily to changes in customer demand) are excluded from inventory and recorded as an expense in the period incurred. We regularly review inventory quantities on hand and record a provision for excess and obsolete inventory based primarily on the estimated . . .