Due to the territorial and administrative division in the war period, information system of health protection after the war was divided in two systems, what matched organisation of health insurance in that period. Those information systems were incompatible, developed on different, both, hardware and software. Therefore, Ministry of Health, within the project "Basic hospital services", financed through the World Bank loan, applied new, common information system in health insurance. Goal of this paper is to present basic features of information system of health insurance in FB&H, as well as the way of its functioning in respect to other institutions included in the system, respective data bases, sites of entering and updating data, while using data available with Federal Bureau of Health Insurance.