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Matejić S. Performance improvement implies acceptance of innovations in all Health care activities including health care financial management. Successful implementation of health care financing reform requires previous costs and activities analysis in health institutions. In the work we performed comparative analysis of the costs of 27 health institutions by applying innovative system for health care services costs analysis and control. Initialy spreadsheet system was made, by using internationaly “Step Down” methodology, for cost control and analisys in the hospitals and was adapted for Primary health care institutions. Results achieved: The dominant cost for employees salaries, on average around 80%, does not depend on the size of Primary health institution (Dom zdravlja); Significant differences in the percentage values of the cost of medicines, medical supplies, diagnostic services; There is an obvious difference percentage values of technical maintenance costs as a result of uneven percentage of the number of non-medical employees, differences in infrastructure organization, the difference in the condition and type of equipment, the difference in the type of space heating and type of fuel for heating, patients transportation obligations especialy of home treatment services and polyvalent patronage.