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The article presents data on biocenotic diagnostics of 12 farms in the Moscow region that are endowed with endometritis and mastitis in cows, as well as gastrointestinal and respiratory diseases of newborn calves, with the aim of identifying zoo-hygienic, zootechnical and veterinary deficiencies to optimize the strategy for dealing with them. Studies on biocenoses were carried out in 12 farms unsuccessful in cows’ obstetric and gynecological diseases, gastrointestinal and respiratory diseases of newborn calves, with a total number of cattle 12 254, including 4445 cows. For this purpose, field trips were periodically carried out for epizootological examinations of farm biogeocenoses and for the selection of blood serum stabilized with heparin and samples of pathological material for bacteriological, mycological, virological, hematological and immunological studies. It was established that in experimental farms there are no proper conditions to ensure the breaking of the epizootic chain during the infectious process. So, the main factors that contribute to the development and spread of these pathologies are poor food supply, violations of elementary veterinary and sanitary rules for keeping and milking, and failure to fully implement measures to prevent these diseases. An analysis of the epizootic situation for cattle diseases caused by conditionally pathogenic bacteria indicates that farms that are unsuccessful for factor infections have all the conditions for the circulation of pathogens, repeated passage through susceptible animals, the increase in the virulence of conditionally pathogenic microorganisms, and in some cases for appearing pathogenicity in saprophytic bacteria. An effective fight against malignant microbial ecosystems requires in-depth knowledge of the parasitocenoses’ quantitative and species composition, the study of relationships between its individual representatives, the mandatory identification of pure cultures of all its members, and determination of the microbial agents marker biological properties, as well as detailed biocenotic diagnosis of the animal habitat (farm, barn, etc.).