The article is devoted to one of actual problems of gastroenterology - study of microbiocenosis of gastrointestinal tract in functional disorders. Functional gastrointestinal disorders (FGID) or minimal dysfunctions of digestion are frequent in the first months of child's life and provoke anxiety both in parents and in pediatricians. Aim: to explore the microbial landscape and the associative structure of the microbiota of the large intestine in children with functional disorders of the gastrointestinal tract. Subjects and methods: Intestinal microbiota composition of 225 children with functional gastrointestinal disorders and 100 healthy children was studied using bacteriological method. Results. The 88.4 % frequency of detection of intestinal eubiosis disorders is discussed. Information is provided on the species composition of the major opportunistic organisms that inhabit this biotope. According to the results, decrease of bifidobacteria amount in structure of large intestine microbiota increases rate of detection of opportunistic microorganisms - predominantly, Klebsiella genus bacteria and Staphylococcus aureus. The intestinal microbial community is dominated by multicomponent transient association. The frequency of detection of pathogenic Staphylococcus in children under one year is discussed in detail. Conclusions. A distinctive feature of the intestinal biocenosis microecological status is significantly greater spread of enterococci than in healthy children, which can be a risk for the emergence of strains with the presence of a number of pathogenecity factors that cause infectious processes.