Abstract: Clinical outcome of Helicobacter pylori infection might be associated with specific virulence-associated bacterial genotypes. The distribution of different bacterial genotypes varies geographically. The aim of this study, is based on determining any associations between the Helicobacter pylori vacA research in causing gastritis and peptic ulcer, in Shahrekord, Iran. Gastric biopsies were collected from patients that were referred to endoscopy unit of Hajar hospital Shahrekord, Iran. H. pylori was detected in these biopsies by culture test. Then polymorphism of vacA gene was genotyped by Polymerase Chain Reaction (PCR). The vacA genotypes were significantly different among gastritis, peptic ulcer and gastric cancer patients. Also, the vacA s1 allele was more frequently identified than the vacA s2 allele among gastrointestinal patients. Furthermore, the severest genotype of vacA gene in these patients was s1/m2. The results of our study illustrated that s1/m2 genotypes were associated with peptic ulceration in patients that infected by H. pylori.