The article provides a brief overview of the main problems and improvement of the system of medical rehabilitation in the sanatorium-resort institutions (SRI) of the Kyrgyz Republic, and also presents the results of treatment, i.e. the effectiveness of rehabilitation measures. In Kyrgyzstan, the initiated process of privatization of sanatorium-resort organizations changed the form of ownership of more than half of state, departmental and public-owned health resorts. In 2000, the share of state ownership in health resort organizations was 49.6% (Data of the Statistical Committee of the Kyrgyz Republic, 2017). We notice that for more than 20 years of independence of the republic, the rehabilitation service has not been able to reach those former heights, there are internal and external factors for this. Even the fact that today in the structure of the authorized body for health protection (Ministry of Health) there is no department that would work on the development of the rehabilitation service of restorative medicine, balneology and sports medicine, which in turn caused the need to analyze and substantiate the activities of the rehabilitation service in health resort institutions.