To elucidate factors associated with the very low risk of gastric neoplasia in Yogyakarta, Indonesia, approximately 1/50 of the level in Japan, we recruited 52 male and 39 female participants from the general populace in the city of Yogyakarta in October 2003. Helicobacter pylori IgG antibodies were found in only 5% (0-13) (95% confidence interval) and 4% (0-9) for Javanese males and females, respectively, and were statistically lower than the 62% (58-65) and 57% (53-60), respectively, in Japanese. Furthermore, positive findings of pepsinogen test were only 0 and 2% (0-6) for males and females, in Yogyakarta, and were again significantly lower than the 23% (22-25) and 22% (20-23), in Japan. The very low incidence of stomach cancer in Yogyakarta may be due to a low prevalence of H. pylori infection and chronic atrophic gastritis.