Although only a minority of the infected individuals develops atrophic gastritis and the malignancy, factors governing clinical outcomes subsequent to Helicobacter pylori (H. pylori) infection have not yet been defined. H. pylori infection is characterized by extensive infiltration of neutrophils. Myeloperoxidase (MPO) in neutrophils amplifies the oxidative potential of hydrogen peroxides that induce gastric mucosal damage, thus MPO is suspected to play a role in H. pylori-induced gastric injury. Therefore, we explored the association of host MPO genetic polymorphism with atrophic gastritis upon H. pylori infection. Biopsy specimens taken from the gastric mucosa were examined histologically in 87 patients. The PCR-RFLP assay was used to characterize MPO genotypes. The distributions of MPO genotypes were MPO (G/G) 82% and MPO (G/A) 18%. None of MPO (A/A) genotype was observed. A strong positive correlation between the levels of neutrophil infiltration and gastric atrophy found only in MPO (G/G) but not in MPO (G/A) genotype. These results suggest that MPO genotype is a critical determinant in the pathogenesis of atrophic gastritis subsequent to H. pylori infection. Further works need to clarify the functional relevance of MPO genetic polymorphisms on gastric cell injury.