Objective: To compare the Helicobacter pylori-associated pathology in gastric biopsies taken from patients living at sea level with those taken from patients living at high altitude. Methods and results: We included 38 patients from a hospital in the Andean city of La Oroya, Peru, located at 3700 m in altitude, and 40 control patients taken from Comas Clinic located in the city of Lima at sea level, Fibrepanendoscopy and multiple biopsies were performed in all the patients followed by histopathological examination. In the antrum, patients from the Andean town had a higher prevalence of glandular lymphoid adherence lesions, active germinal centres, moderate to severe chronic atrophie gastritis, intestinal metaplasia and moderate to severe total deep gland loss, than did patients from the coastal town. Furthermore, the severity of the histological lesions seen in the gastric body and cardia was significantly greater in the high-altitude patients than in those from sea level. Conclusion: This study suggests that the severity of H. pylori-associated gastric lesions seen on histopathological examination is greater in patients living at high altitude, the cause of which is most probably multifactorial but nonetheless principally altitude related. © 2005 Blackwell Publishing Limited.