Investigation of gastric and colon microbiota in Helicobater pylori-infectes patients shown that: 1. Gastric microbiota in H. pylori-positive and H. pylori-negative patients was different and the samples from H. pylori-positive patients were characterized by the higher growth of opportunistic bacteria; 2. The link between H. pylori in stomach and colon microbiota is possible; 3. After eradication without probiotics we saw decreasing level of Bifidobacteria spp., Lactobacillus spp. and increasing level of opportunistic bacteria and Candida albicans but in case of additional usage of probiotics the colon microbiota is better after treatment. Perhaps it is needing to perform future studies to confirm our results.