The association between Helicobacter pylori infection and tooth loss has been studied in Western countries; however, this relationship remains controversial. Although the prevalence of H. pylori infection is higher and atrophic gastritis is usually observed in patients with H. pylori infection in Japan unlike that in Western population, no study has examined the association between H. pylori infection and tooth loss. We examined 959 healthy adults who participated in a mass survey. We counted the number of residual teeth and measured both H. pylori stool antigen and serum anti-H. pylori antibodies. Serum pepsinogen levels were measured to determine the presence of atrophic gastritis. Multiple logistic regression analysis was performed after adjustments for age, body mass index (BMI), smoking and alcohol habits, and educational background. In men, H. pylori infection was a significantly reduced risk factor for loss of all the teeth even after adjustments for other factors (OR, 0.32; 95% CI, 0.12–0.81; P < 0.05). However, such an association was not found in women (0.91; 0.49–1.69). The calculated OR for the presence of atrophic gastritis among individuals with tooth loss was not significant in both men and women. H. pylori infection was associated with a decreased risk of tooth loss in healthy Japanese men.