Background and Objective: BabA2 and Hpa genes are involved in adherence of Helicobacter pylori (H.pylori) to gastric mucosal tissue. This study aimed to investigate the frequency of these genes in isolates of H. pylori from gastric biopsies and their relationship with gastritis, peptic ulcer and gastric cancer.Methods: Gastric biopsy samples were obtained from patients with gastritis, peptic ulcer and gastric cancer. A sample was sent to the laboratory for urease test and histopathology study, and another sample for DNA extraction. The frequency of BabA2 and Hpa genes was investigated using their specific primers by PCR.Results: Among the 80 analyzed biopsy samples, 51 (63%) were BabA2 positive, and the frequency of this gene in the samples of gastric cancer, gastritis and peptic ulcer was 61.1, 58.3 and 73.3%, respectively. In addition, 57 samples (71%) were Hpa positive, and the frequency of this gene in the samples of gastric cancer, gastritis and peptic ulcer was 55.5, 69.4 and 84.6%, respectively. There was no significant correlation between the presence of these genes and the type of H.pylori-related diseases.Conclusion: Frequency of BabA2 and Hpa genes is higher in the samples of peptic ulcer but there was no significant relationship between these genes and H.pylori-related diseases.Keywords: BabA2, Hpa, Gastric Cancer, Gastritis, Peptic Ulcer. Data were analyzed using SPSS software (version 18) and described using percentages and ratios. The chi-square test was used to compare groups and P-value of <0.05 was considered as statistical significance level.