An approach to increase effectiveness of epidemiological control of Crimean hemorrhagic fever, West Nile fever and Astrakhan spotted fever by building a prognostic model of epidemic activity based on contemporary information technologies of spatial and intellectual data analysis was developed and tested. Personified data on 4505 laboratory confirmed cases of natural-focal infectious diseases registered in the Russian Federation and database on 1999 - 2011 climatic observations were processed. A model implementing prognosis of epidemiological situation intensity level as a function of a combination of factors, maps of density of epidemic manifestations were built. On a practical example high effectiveness of the approach to epidemiological analysis based on the use of contemporary analytical technologies for evaluation of temporal and spatial categories of epidemiological risk was demonstrated.