Introduction. The annual growth of medical waste due necessitates a comprehensive approach to solving the issue of medical waste management. It is necessary to develop unified methodical strategies for the complex solution. The objective of the study. To substantiate the hygienic efficiency of the thermal decontamination of class B and C medical waste based on geo-informational system (GIS) technologies in the Krasnoyarsk region for five consecutive years. Materials and methods. Medical institutions (MI) of the Krasnoyarsk region’s three macro districts were studied as class B and C waste sources. At the first stage, the composition of wastes by classes and their volumes were determined, and local technologies of thermal deactivation available in medical organizations were identified. The received information was subjected to statistical processing, stratified on electronic maps to apply GIS technologies further. Results. Based on statistical processing of data on medical class B and C waste generation in separate MO, the analysis of operating technologies capacity in 2014-2015 based on GIS-technology of spatial analysis, construction of optimal transport ways of waste delivery, area mapping in the three districts in the Krasnoyarsk region have been substantiated proposals to optimize medical waste management for five years. Conclusion. To have an environmentally and epidemiologically safe system of handling class B and C waste in the region, it is necessary to create a comprehensive functional model based on GIS technology, taking into account the optimal combination of decentralized and centralized systems, regional features of the transport network, and the prospects of health care system development.