The article presents data of detailed biocoenotic diagnostics in 12farms of the Moscow region affected by obstetric-gynecologicdiseases of cows (endometritises, and mastitises), as well asgastrointestinal and respiratory diseases of newborn calves with theaim of identifying zoo-hygienic, zootechnical and veterinarydeficiencies to optimize a combat strategy against factor infections. Tothis end, periodic visits were made to farms for epizootologicalexaminations of farm biogeocenoses and the selection of bloodserums, heparin-stabilized blood and samples of pathological materialfor bacteriological, mycological, virological, hematological andimmunological studies.An analysis of the epidemiological situation for cattle diseases causedby conditionally pathogenic bacteria shows that in farms of theMoscow region, where factor infections are unfavorable, there areconditions for the circulation of pathogens, multiple passage throughsusceptible animals, increased virulence of conditionally pathogenicmicroorganisms, and in some cases, the emergence of pathogenicityin saprophytic bacteria. It is shown that the main factors contributingto the development and dissemination of these pathologies are theunsatisfactory food basis of farms, violations of elementary veterinaryand sanitary rules for keeping and milking, failure to fully implementmeasures to prevent these diseases due to the lack of sufficientmaterial resources in the farms. All the above demonstrates thatexperienced farms are lacking adequate conditions to ensure theepidemiological chain in the infectious process.Effective control of malignant microbial ecosystems require in-depthknowledge of the quantitative and species composition ofparasitocenoses, the study of relationships between its individualrepresentatives, 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 animalhabitat (farming, barn, etc.).