This article presents the results of original research conducted in St. Petersburg, Russia, which showed that the Helicobacter pylori strains isolated from patients with duodenal ulcer and chronic gastroduodenitis possess significantly higher levels of the pathogenicity islands (cag-PAI) genes than the strains isolated from healthy volunteers. The most frequently detected cag-PAI genes were cagA and cagH in the strains isolated from patients with chronic gastroduodenitis, and cagA and cagE in the strains isolated from patients with duodenal ulcer. A comparison of the clinical strains isolated from patients from St. Petersburg, Russia and patients from Dushanbe, Tajikistan showed that cagA gene was more prevalent in the strains from St. Petersburg. These findings demonstrate the necessity of implementation of molecular genetic identification of H. pylori in the clinical diagnostics practice reflecting the virulent genes profile of the strain. Addition of probiotics to the standard eradication therapy of H. pylori significantly improves the results of this therapy.