This specialist diploma thesis entitled Specifics of Accounting in the Health Care System provides research related to the health care system and its costing, and includes a particular cost analysis for a general practitioner’s office and one dental practice. The paper discusses non-profit and for-profit organizations related to the health care system, with particular emphasis on cost management, which has become increasingly important for the purpose of cost reduction on the one hand and improving the quality of health care for the patient on the other. A non-profit organization is an organization whose goal is not profit but providing the best possible services relative to available funding, and whose success is measured through differentiated performance. A for-profit organization is an organization whose goal is to make a profit. The health care system in Croatia is financed from the state budget and tax contributions, it is mandatory and accessible to all citizens, as it is based on the idea of solidarity between the healthy and the sick, the rich and the poor, the young and the elderly. The patient is at the center of the health care system, with special attention being paid to vulnerable groups (children, women, the elderly, persons with special needs). Primary health care services are an important part of the entire health system; in other words, these services signify an individual’s first contact with the health care system. Nowadays in the health care system, more and more focus is placed on cost management in order to reduce the staggeringly high expenditures within healthcare. Treatment costs might be reduced if more money were to be invested in early disease detection, improved diagnostics, and illness prevention. Cost management is extremely important for the health system to succeed; namely, improving treatment outcomes with no change or decrease in expenditures, all in order to increase the value of provided health services for the patient.