The paper describes the procedure for analyzing the specialized medical care payment system at the level of the subject of the Russian Federation, which is based on the step-by-step analysis of the tariff agreement of a subject of the Russian Federation, on the medical care payment model used in a day or round-the-clock hospital, on the medical care provided in the context of care conditions, nosological entities, clinical and statistical groups of diseases and healthcare facilities according to the registers of accounts, on the correctness of coding of treatment cases in the clinical and statistical groups, and on the average cost intensity ratio and duration of therapy for patients. The presented procedure divides all the stages into two main sections, one of which is the analysis of regional normative legal acts for compliance with their federal documents and for identification of the main regional features of the specialized medical care payment system; and the other is the analysis of health care registers that can be used to assess the actual provision of medical care, achievement of planned indicators and the actual deviation of the rendered care from the statutory norms in the regional and federal normative legal acts. Each stage of the analysis is described in detail; possible works within the stage and the results that can be obtained during the analysis are considered.