The article presents qualitative and quantitative parameters of microbiocenosis of oral fluid and feces of clinically healthy children in different age groups. In most of the cases compensated disbiotic changes were found, which were characterized by reduction in the number of indigenous microflora (lactobacilli and bifidobacteria) and increase of representatives of opportunistic pathogens (Staphylococcus, Bacillus and Candida). Microecological changes in different gastrointestinal biotopes are closely interrelated. Saliva may be considered as a specimen of integral fluid of human environment and can be used for complex assessment of the state of gastrointestinal tract microflora.