Autoprobiotic applications based on Enterococcus faecium in clinical practice have been researched on a group of patients with irritable bowel syndrome (IBS). We examined 50 patients with IBS aged 22 to 55 years. In order to objectify the research, patients were randomly assigned into 2 groups: - patients of the first group (25 people) received lactic acid starter culture containing 108 CFU / ml of own enterococci (Enterococcus faecium) in 1 ml of starter culture, at a dose of 100 ml / day 50 ml twice a day for 10 days); - patients of the second group received lactic acid starter culture containing Enterococcus faecium L3 in a titer of 108 CFU / ml) with a dose of 100 ml / day (50 ml twice a day for 10 days). Clinical evaluation of the effect of probiotic therapy on the condition of patients with IBS was carried out on the basis of the dynamics of severity such typical symptoms of IBS, as the severity of abdominal pain, discomfort in the epigastric region, flatulence, stool characteristics according to the Bristol scale (BS). Also, the rated preservation of appetite and general state of health were assessed by the patient. During the follow-up examination of patients after the course of treatment there was noticed a significant improvement in all clinical parameters in both groups which corresponds to the data of scientific research. At the same time, significant differences were observed in the dynamics of some indicators of the two comparison groups. So, in a group of volunteers who received an autoprobiotic, flatulence was significantly less pronounced (the main cause of which is the excessive growth of conditionally pathogenic flora). Also on the background of the application of the claimed product became significantly less pronounced such clinical manifestations of IBS as abdominal pain (0.41 ± 0.15 versus 0.87 ± 0.15 log in the Enterococcus faecium L3 group), a feeling of heaviness in the abdomen (0.37 ± 1.14 versus 0.79 ± 1.17 log). Microbiological examination of the state of intestinal microbiocenosis of the observed patients revealed that both after the course of treatment with lactic acid starter culture based on the Enterococcus faecium L3 strain, and after treatment with an autoprobiotic, the state of the microflora significantly improved. More significant changes occurred after the course of autoprobiotic therapy: 1. There is a significant decrease in the number of opportunistic enterobacteriaceae from 0.87 ± 0.38 to 0.12 ± 0.12 log (p = 0.04). 2. The number of bifidobacteria significantly increased from 7.79 ± 0.28 to 8.95 ± 0.04 log (p = 0.0009). 3. The number of lactobacilli significantly increased from 7.83 ± 0.21 to 8.95 ± 0.04 log (p = 0.0007). 4. The number of enterococci significantly increased from 4.91 ± 0.11 to 5.83 ± 0.20 log (p = 0.002). 5. The number of E. coli significantly increased from 6.12 ± 0.19 to 6.41 ± 0.17 log (p = 0.005). As a result of numerous approbations of the claimed method, the preparation time of a probiotic product obtained on the basis of Enterococcus faecium autostrains is significantly reduced, which, in comparison with similar biotechnological probiotics, is an original, effective and safe remedy for the treatment of dysbiosis of any etiology.