Abstract: Objective To investigate the relationship between Helicobacter pylori (H.pylori) vacuolating cytotoxin gene A (vacA) s1m2 and intestinal metaplasia (IM) of gastric mucosa in gastropathic patients and to provide evidences for the treatment of H.pylori infection-associated atrophy gastritis and the prevention of gastric cancer.Methods A total of 271 H.pylori-positive paraffin-embedded biopsy specimens of gastric mucosa were collected among 76 superficial gastritis (SG) patients (18 with IM),56 atrophic gastritis (AG) patients (37 with IM),and 139 gastric ulcer (GU) patients (30 with IM).Formalin-fixed,paraffin-embedded (FFPE) DNA kit was used to extract DNA of the specimens and the genotype of vacA s1m2 was analyzed with nested PCR and agarose gel electrophoresis.Results The detection rate of vacA s1m2 in AG patients was 53.6% (30/56) and significantly higher than that in SG and GU patients.In the 271 H.pylori-positive cases,the detection rate of vacA s1m2 in all the patients with IM was 62.4% (53/85) and significantly higher than that in the patients without IM.Moreover,the detection rate of vacA s1m2 in AG patients with IM was 75.7% (28/37) and significantly higher than that in the AG patients without IM and in GU with IM.Conclusion H.pylori vacA s1m2 is closely related to IM among gastropathic patients,especially in the atrophic gastritis patients,suggesting that H.pylori strains with vacA s1m2 may be considered as a highly pathogenic strain for atrophic gastritis.