Helicobacter pylori infection is now accepted as the major cause of severe gastritis-associated diseases, including peptic ulcer and gastric cancer. In the current study, we decided to determine the dupA and OipA genotypes in H. pylori strains isolated from patients with gastrointestinal disorders and to evaluate whether these genes are associated with the severity of the gastroduodenal diseases. We obtained 100 H. pylori positive specimens from 296 patients by endoscopic biopsy. The prevalence of genotype was assessed by PCR and related to clinical histopathological parameters. The dupA and OipA positive strains had a prevalence of 39% and 57% respectively. In our cohort, there was no significant relationship between dupA genotype and peptic ulcer disease (P=0.98). However, there was a relationship between dupA- strains and gastric cancer (P=0.019). We were unable to identify association between OipA+ genotype and clinical outcome (P=0.145). The relation between dupA, and OipA, positive genotype as a single genotype and the development of cases to gastric cancer was statistically significant (P<0.001). According to the results, the presence of dupA gene can be considered as a marker for the gastric cancer; however, the OipA gene cannot be regarded for prediction of peptic ulcer and gastric cancer.