The article shows the experience of the Republican Bureau of Forensic Medical Expertise of the Ministry of Health of Tatarstan Republic in organizing and ensuring anti-epidemic measures using a quality management system. The comprehensive implementation of anti-epidemic measures in the expert institution dictates the need for regulation of the main provisions by internal documents (standard operative procedures), built on the basis of existing regulatory legal acts. The method of quality management system based on the Shekhard-Deming cycle was applied in practical activities, a process-based approach was used to organize work in organization. The proposed standard operative procedures, together with a model for managing the activities of an epidemiologist, showed high efficiency and allow improving the process of managing epidemiological risks.