This study enrolled 92 clinical strains (45 from peptic ulcer, 27 from gastritis, and 20 from gastric cancer) to detect whether the babA and babB are at locus A or B by PCR reactions using the primers designed from the upstream and variable region of the babA and babB genes. Four genotypes of babA and babB (A B, AB B, A AB, AB AB) were found. The distribution of the 4 genotypes in 92 clinical strains was significantly different among patients with different gastric diseases (p<0.05). The isolates from gastric cancer patients had a higher rate of AB AB genotype than those from non-cancer patients (40.0% vs. 9.7%, p<0.05). The AB AB genotype was associated with a higher intensity of intestinal metaplasia (p<0.05), but did not correlate with a higher inflammation and colonization density in gastric histology (p>0.05). Besides, the study enrolled 19 patients to verify whether variable genotypes of babAB existed in the different gastric niches. Among the patients infected with more than one babAB genotypes over antrum and corpus, there were higher rate of genotypes as A B or AB AB in isolates from antrum than in those from corpus (75.0 % vs. 16.7%, p<0.05).