Geographical distribution of individual genotypes of Helicobacter pylori, predominance of virulent types in various regions of Russia, particularly in the Prymorye Territory, remains unclear. We examined 115 children with various gastroduodenal pathology and 33 patients with gastric cancer, of which 57.39 and 60% respectively were infected with H. pylori. All samples positive for H. pylori were further analyzed for gene vacA mosaicism. In all clinical subgroups, variants s1 and m1 predominated; the frequency of genotype s1 was significantly increased (1.3-fold) in the group of cancer patients in comparison with the group of children with gastroduodenal pathology. Three variants of allele combination of signaling and middle regions of the vacA gene (s1m1, s1m2, and s2m2) were revealed; s1m1 was the most frequent in both groups. We suggest that this genotype is a marker of complicated course of gastroduodenitis and a factor of gastric cancer development in local population.