Problems of detailed studies into the epizootic process of infectious diseases of farm animals, mechanisms of interaction of pathogenic microorganisms with macroorganisms, as well as issues of health improvement and protection of animal populations from epizootically significant diseases are acute for veterinary science and practice. As a result of the studies the spectrum of pathogens in parasite cenosis on the territory of the entity of the Russian Federation was identified. The species composition of pathogens in cases of non-infectious pathology and infectious diseases in young cattle is specified. The pathogens are represented by Staphylococcus spp., Streptococcus spp., E. coli. K-99, pathogenic fungi Aspergillus spp.and yeast fungi Candida albicans, BHV-1 and BVDV. A database was compiled to upgrade the methodology of analyzing epizootological studies. The development and implementation of health and health-related programs has decreased the occurence of acute intestinal infections and respiratory tract infections in young cattle by more than 1.3 times. Multi-level epizootic surveillance of farm animal populations can prevent the occurrence and spread of particularly dangerous infections, eliminate managed infections, downgrade the risk of post-infectious complications and improve the economic efficiency of the livestock industry as a whole.