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Evaluation of the territories of the Russian Federation (RF) on the degree of risk of the disease of focal disease and the development of appropriate methods is the actual problem. Some provisions of a known methodology of calculation of «index of integral nosogenity of territory» (Malkhazova, 1998) can be applied in this work. The average long-term data of official statistics in the incidence of seven diseases selected as model (leptospirosis, tularemia, malaria, psittacosis, West Nile fever, diphyllobothriasis and opisthorchiasis) was used during the development and approbation of the proposed methodology. For each disease the ranges of the average values of incidence were divided into three categories – "points of significance", similar to the above method. This was done by means of GIS, using the tool "breaks on natural groups’ ranks". Level of morbidity expressed in tabular form for all the subjects of the Russian Federation is the basis for the risk analysis of disease natural-focal diseases in Russia's regions. On the basis of the calculations results the maps of incidence for all the subjects of the Russian Federation as well as synthetic map of the integral degree of risk of the disease of model disease to subjects of the Russian Federation with indication of number of diseases (from seven model diseases) and the total level of morbidity in the region were created. Preliminary analysis and generalization of results to larger territories - Federal districts and the Russian Federation as a whole were