Helicobacter pylori and hepatitis A virus (HAV) share a common fecal-oral transmission route. The aim of this study was to investigate the prevalence of and risk factors for H. pylori and HAV infection in primary school students in Taiwan. We studied 289 Grade 1 to 6 students from a single primary school in Taipei County in 2003. The students volunteered for blood tests for H. pylori immunoglobulin G (IgG) antibody and anti-hepatitis A antibody after consent from their parents. Questionnaires were administered to the parents to investigate possible risk factors. The seroprevalence rates of H. pylori IgG antibody and anti-hepatitis A antibody were 21.5% (62/289) and 1.4% (4/289), respectively. No statistically significant relationship was found between seropositivity for H. pylori and for HAV. If parents had knowledge of H. pylori and HAV, their children were significantly more likely to be seronegative for H. pylori (p=0.020, odds ratio [OR] 2.1, 95% confidence interval [CI] 1.2-3.7) and HAV (p=0.012, OR 11.2, 95% CI 1.5-83.4). Students whose family members had no history of HAV infection were significantly less likely to be seropositive for HAV (p=0.001, OR 0.04, 95% CI 0.004-0.5). No other factors were found to be significantly associated with seropositivity, including blood type; age; gender; family members' history of H. pylori infection; travel to China; parents' educational level; sources of water supply; family members' use of tobacco, alcohol, or betel nut; family members' history of peptic ulcer or gastritis; and students' history of recurrent abdominal pain. Lack of public health knowledge appears to be related to seroprevalence of H. pylori in primary school students. The low seroprevalence of anti-HAV antibodies demonstrates the lack of protection against this infection in school-age children in Taiwan and suggests that universal administration of HAV vaccine would be wise.