The microflora of 64 biopsies taken during fibrogastroduodenoscopy of the mucous membrane of the esophagus, stomach and duodenum in healthy volunteers and 1120 samples obtained from the same parts of the digestive tract in patients with esophagitis, chronic gastritis and peptic ulcer disease were studied. The patients ranged in age from 18 to 62 years. Traditional bacteriological method was used to isolate and identify microorganisms. Staphylococcus spp., Streptococcus spp., Lactobacillus spp., Bacteroides spp., Stomatococcus spp., Enterobacteriaceae, Corynebacterium spp., Micrococcus spp., Neisseria spp., Veilonella spp. were isolated from biopsies of healthy respondents in an average amount from 3.2 to 4.68 lg CFU/g. H.pylori was found in 60% (5.66 lg CFU/g) in the esophagus, in 33.3% of cases (5.12 lg CFU/g) from the fundal part of the stomach, in 44.4% (5.25 lg CFU/g) from the antral part of the stomach, in 5.5% (4.2 lg CFU/g) in the duodenal mucosa. In samples obtained from the inflamed and eroded mucous membrane of the esophagus, stomach and duodenum, opportunistic bacteria of the genera Klebsiella, Enterobacter, Proteus, Pseudomonas, Peptococcus, Actinomyces, yeast fungi of the genus Candida etc. were detected in an amount exceeding 4 lg CFU/g. H. pylori isolated in 6.3-16.7% of patients (4.25-4.6 lg CFU/g) and did not dominate in relation to other microorganisms, and in most cases had a low frequency of its occurrence. In patients with the recurrence of peptic ulcer disease, exacerbation of chronic gastritis and esophagitis, dysbiosis was developed, characterized by an increase in the species and quantitative composition of opportunistic microflora, an increase in its enzymatic and cytotoxic activity, which can contribute to the maintenance of inflammatory and necrotic processes and inhibit the elimination of the pathological process.