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Helicobacter pylori is the major cause of active chronic gastritis and peptic ulcers in humans and has been linked to gastric carcinoma and lymphoma. The vacuolating cytotoxin vacA and cag pathogenicity island (cag PAI) are two identified virulence factors that are considered to have an important role in the pathogenesis of H. pylori infection. The aim of this study is to investigate the H. pylori vacA alleles in Iranian patients with peptic ulcer disease. In order to investigate this, biopsy specimens were obtained from 84 patients with gastric ulcer, gastritis, and duodenal ulcer. DNA extraction and PCR were used to detect the presence or absence of glmM, cagA and to assess the polymorphism of vacA. Of the 77 glmM PCR-positive biopsy specimens, 55 (71%) had the vacA signal sequence genotype s1, and 22 (29%) had subtype s2. vacA mid-region analysis revealed that 31 (40%) were vacA m1 and 46 (60%) were m2. The presence of the cagA gene correlated with vacA signal sequence type s1, whereas type s2 was predominantly found in cagA-negative samples (P < 0.001). Thus, the detection of vacA and cagA, virulence markers described in several clinical outcomes may be used to help the treatment and prevention of H. pylori in Iran. [ABSTRACT FROM AUTHOR]