In Russia, as in other countries, the problem of emerging natural focal infectious diseases (EIDs) became more acute toward the end of the 20th century. However, the situation in Russia is unknown to foreign readers, while the prevention and control of these diseases require international collaboration. The aim of the study is to provide a medical-geographical assessment of the distribution of the main natural focal EIDs in Russia, as well as to present the approaches used in the country to create aggregate maps of risk assessment. To consider its current status, we determined the most important natural focal EIDs for Russia (tick-borne encephalitis, ixodid tick-borne borrelioses, hemorrhagic fever with renal syndrome, Crimean-Congo hemorrhagic fever, West Nile fever, Astrakhan spotted fever, leptospiroses, and tularemia) and analyzed the patterns of their epidemic manifestation. As a result, a working classification of such infections and a series of maps showing the current situation of EID morbidity in Russia were created. To design an aggregated risk map, we developed an original mapping methodology and recalculated the model disease incidence by taking data from administrative units and adjusting them for natural geographical boundaries (biomes) for European Russia, and then evaluated the risk of infection for separate model diseases and for a set of them. The highest risk rates are confined to the northwest regions of European Russia, the Cis-Urals and the Volga region, which are naturally related to forest biomes, as well as to the southern steppe regions of the interfluves between the Volga and the Don, and the foothills of the North Caucasus.