Several virulence factors of Helicobacter pylori may contribute to gastric mucosal damage. In this study, the prevalence of cagA and vacA genotypes of H. pylori was examined in different patterns of chronic gastritis. Oesophagogastroendoscopy was performed in 147 dyspeptic patients. Antrum biopsies were obtained for isolation of H. pylori and for histopathological assessment. H. pylori vacAs1 and cagA genes were directly genotyped in the gastric biopsy specimens by polymerase chain reaction (PCR). A total of 102 dyspeptic patients, all H. pylori-positive by PCR, were included in the study. Of these, 59 had active chronic gastritis and 37 had non-active chronic gastritis. The prevalence of cagA and vacAs1 was higher among patients with active chronic gastritis than among those with non-active chronic gastritis (45.8% vs 21.6% (p = 0.02) and 78.0% vs 40.5% (p < 0.001), respectively). In conclusion, both cagA and vacAs1 genotypes are associated with the activity of chronic gastritis.