The Faculty of Geography, M.V. Lomonosov Moscow State University, is creating a "Natural Focal Diseases" medical and geographical atlas of Russia. The paper considers the possibilities of the atlas to monitor and assess the epidemiological situation of a number of diseases. The atlas allows one to define a spectrum of the most epidemically significant natural focal diseases in Russia, to quantitatively characterize their incidence in the population, and to visualize it in a series of maps, to make a medical geographical analysis of the prevalence of the nosological entities of natural focal diseases in both individual subjects of the Russian Federation and in Russia as a whole. By using tick-borne encephalitis as an example, the authors consider approaches to analyzing the incidence of natural focal infections, by using different types of the maps given in the atlas.