Peculiarity origin and pathogenesis of the disease of digestive and respiratory organs of agricultural newborn animals first of all depends on changes of microbiocenosis organs, reduction activity of clostral immunity and natural steadiness of body, increasing receptive to the disease agents.The result of research shows that in most cases the solution of neonate animals appears in the result of reduction enumeration and quantity of useful microorganisms, increasing quantity of gram-negative and gram-positive microbes such as Escherichia, staphylococci, proteia, salmonella, clostridium and others.The factors causing to strengthening of diseases are the mistakes in the measures of animals storage hygiene, feeding technological stresses and other factors.