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Objective The main goal of this study is to measure the impact of two alternative methods of overhead cost allocation of chilean public hospitals into the final production cost of 256 health care services which are recurrent in health problems whose burden of disease is high in Chile. Methods A purposively sample of six important hospitals of metropolitan region in Chile was considered. A survey was applied to them in order to collect analytic cost data of resource use (labor, medical supplies and use of capital) in the production of health care services. The data of overhead cost (electricity, central heating, laundry, administrative support, transport, maintenance, etc.) were obtained from the Information System of each hospital. The final cost of each health care service was calculated from the perspective of health public system, in two ways: (1) using a proxy rate of common use, and (2) using overhead cost rates as a result of a step-down methodology. The final costs calculated with each method were compared and analized. Results Considering that the gold standard method for allocation of overhead cost is the step-down methodology, the results using proxy rate revealed that 185 services (72,3%) are under costing, and 71 health care services (27,7%) are over costing. Conclusion The use of proxy rates to allocate overhead costs into the final cost lead to important under costing and over costing of health services. This finding is important at least by two reasons: (1) for the management of hospitals, (2) in economic evaluations, the variations in cost can modify the ratio of cost-effectiveness, cost-utility or cost-benefit, influencing the health public decision.