Background/aim: Helicobacter pylori is a pathogen that colonizes a majority of the world's population. Genetic diversity within the virulence genes of bacteria such as cagPAI and vacA may have a modified effect on the pathogenic potential of the bacteria. This study aimed to investigate which genes can be suggested as potentially related virulence factors for H. pylori-associated active chronic gastritis and stomach adenocarcinoma in the northwest of Iran and south of Turkey. Materials and methods: Formalin-fixed, paraffin-embedded stomach biopsy tissue samples were obtained from Iranian and Turkish patients from selected geographical regions. The prevalence of selected cagPAI genes and vacA genotypes were studied in H. pylori-positive samples by using polymerase chain reaction and specific primers. Results: Out of 320 patients, H. pylori was detected in 28.43% of patients. We found that the vacAs1, vacAm2, and cagA genes with mean prevalences of 82.41%, 71.42%, and 69.23%, respectively, were dominant in Iranian and Turkish patients. Conclusion: In the south of Turkey and northwest of Iran the studied genes were homogeneous and there were no significant differences in bacterial genetics. The results of this study indicate that cagA and vacAs1 are dominant genes in people with gastric disorders in our selected geographical regions.