The article presents data of detailed biocoenotic diagnostics in 12 farms of the Moscow region affected by obstetric-gynecologic diseases of cows (endometritises, and mastitises), as well as gastrointestinal and respiratory diseases of newborn calves with the aim of identifying zoo-hygienic, zootechnical and veterinary deficiencies to optimize a combat strategy against factor infections. To this end, periodic visits were made to farms for epizootological examinations of farm biogeocenoses and the selection of blood serums, heparin-stabilized blood and samples of pathological material for bacteriological, mycological, virological, hematological and immunological studies. An analysis of the epidemiological situation for cattle diseases caused by conditionally pathogenic bacteria shows that in farms of the Moscow region, where factor infections are unfavorable, there are conditions for the circulation of pathogens, multiple passage through susceptible animals, increased virulence of conditionally pathogenic microorganisms, and in some cases, the emergence of pathogenicity in saprophytic bacteria. It is shown that the main factors contributing to the development and dissemination of these pathologies are the unsatisfactory food basis of farms, violations of elementary veterinary and sanitary rules for keeping and milking, failure to fully implement measures to prevent these diseases due to the lack of sufficient material resources in the farms. All the above demonstrates that experienced farms are lacking adequate conditions to ensure the epidemiological chain in the infectious process. Effective control of malignant microbial ecosystems require in-depth knowledge of the quantitative and species composition of parasitocenoses, the study of relationships between its individual representatives, required isolation of pure cultures of all his affiliates, the determination of marker biological properties of microbial agents, and the conduct of a detailed biocenotic diagnosis of the animal habitat (farming, barn, etc.). © Advanced Scientific Research. All rights reserved.