Vacuolating cytotoxin is an important virulence factor in H. pylori infection. Cytotoxin-producing H. pylori were more prevalent in patients with severe atrophic gastritis and cytotoxin activities in H. pylori isolates from patients with severe atrophic gastritis were much higher than those from patients with mild atrophic gastritis. It has also been suggested that there are host-related immunogenetic factors for susceptibility or resistance to diseases caused by H. pylori. The allele frequency of HLA-DQA1*0102 was significantly lower in the H. pylori(+) atrophic gastritis and H. pylori(+) intestinal type gastric adenocarcinoma than in the H. pylori(-) normal control and H. pylori(+) superficial gastritis. The HLA-DQA1*0102 allele may contribute to resistance against H. pylori-associated gastric atrophy and its association with intestinal type gastric adenocarcinoma.