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The services of general interest provided by hospitals, such as free HIV clinics, have been funded since 2005 by a lump sum covering all costs. The allocation of the budget was initially determined based on historical and declarative data. However, the French Ministry of Health (MoH) recently outlined new rules for determining the allocation of financial resources and contracting hospitals for each type of services of general interest provided. The aim of this study was to estimate the annual cost of a public free anonymous HIV-testing center and to assess the budgetary implications of new financing systems. Three financing options were compared: the historic block grant; a mixed system recommended by the MoH associating a lump sum covering the recurring costs of an average center and a variable part based on the type and volume of services provided; and a fee-for-services system. For the purposes of this retrospective study, the costs and activity data of the HIV testing clinic of a public hospital located in the North of Paris were obtained for 2007. The costs were analyzed from the perspective of the hospital. The total cost was estimated at 555,698 euros. Personnel costs accounted for 31% of the total costs, while laboratory expenses accounted for 36% of the total costs. While the estimated deficit was 292,553 euros under the historic system, the financial balance of the clinic was found to be positive under a fee-for-services system. The budget allocated to the HIV clinic under the system recommended by the MoH covers most of the current expenses of the HIV clinic while meeting the requirements of free confidential care.