The first part of the paper analyses the financial indicators in the health care system of the Federation of Bosnia and Herzegovina. The structure of total expenditure of compulsory health insurance in the period 2003-2008 was analysed by comparing the financial reports stipulated in the health care system of the Federation of Bosnia and Herzegovina with some foreign financial indicators. According to the existing situation, the objectives and measures required for their full implementation in the following medium-term period 2009-2013 have been determined. The movements of financial indicators following the implementation of certain institutional measures have been estimated according to the flow of some indicators from the previous period (time series) and in accordance with the global trends of some macroeconomic indicators (employment, GDP, etc.).