The aim of the study was to identify the features of the influence of autoprobiotic and probiotic E. faecium strains on clinical and laboratory parameters in children with functional gastroenterological pathology. Patients and methods. In the period 2020–2021. 35 children over 3 years of age with functional gastrointestinal disorders (FGID) were observed on an outpatient basis, who were prescribed an autoprobiotic or probiotic strain E. faecium for therapeutic purposes and recommended a diet. The study protocol provided for clinical and anamnestic screening, FGID diagnostics; analysis of coprograms and assessment of the composition of the intestinal microbiota in children before and after a course of probiotics. The study of intestinal microbiota was carried out by RT-PCR in feces using a set of primers “Colonoflor”. One patient was excluded from the study due to refusal to take the autoprobiotic. The rest of the patients formed two groups: group 1 (n = 16) — children who received the autoprobiotic strain and group 2 (n = 18) — children who received the conditionally “reference” strain E. faecium L3. Probiotics were used in the form of a liquid form (which is a starter culture based on soy protein isolates containing 10⁹ CFU in 1 ml) at a dose of 25 ml 2 times a day for 10 days. The results of using probiotic strains were evaluated on the basis of data from a survey of parents about the state of children and the dynamics of clinical manifestations, as well as changes in the values of indicators of coprograms and the composition of the intestinal microbiota. Statistical processing of the results was carried out using Student’s t-test, Mann-Whitney U-test; Wilcoxon test. The results were considered reliable at a significance level of p <0.05. Results. Studies of the effect of prescribing E. faecium L3 strain and an autoprobiotic strain to children with FROP revealed a positive effect on the clinical symptoms of the disease (in 29.4% and 25%, respectively) in the absence of undesirable side effects. Analysis of the dynamics of coprograms revealed an equivalent positive dynamics in the form of improvement in most of the studied stool characteristics. The study of the composition of the intestinal microbiota in the observed children revealed a low level of Lactobacilli and Enterococcus before and after the administration of probiotics. After the course of the E. faecium L3 strain, a significant increase in the content of F. prausnitzii was noted. The use of an autoprobiotic strain contributed to a significant decrease in the frequency of isolation of conditionally pathogenic bacteria in large numbers Conclusion. The course appointment of autoprobiotic and probiotic E. faecium strains in children with FGID has a positive effect on clinical symptoms, improvement of most coprogram indices and normalization of the intestinal microbiota composition.