Analysis of zoonotic and natural-focal infectious disease morbidity in 2009 - 2011 in Siberia and the Far East is presented, and a complex of measures aimed at their prophylaxis is proposed. Analysis is carried out based on the data received by Reference Center of Monitoring of Natural-Focal Infection Causative Agents and Regional Center of Monitoring of I-II Pathogenicity Group Causative Agents at the Irkutsk Research Institute of Plague Control from departments and Centers of Hygiene and Epidemiology of Siberian, Far Eastern, 3 subjects of Urals Federal District and 5 Stations of Plague Control of Federal Service for Control in the Sphere of Protection of Consumers' Rights and Well-Being of Humans. In the morbidity structure in this region "tick-borne" infections were established to predominate--69.4%, among bacterial--yersiniosis dominates. Deterioration of epizootic situation on rabies is observed in the Republics of Tuva and Buryatia.