Background Helicobacter pylori infection is a common infection. Risk of infection in rural areas is six times higher than in urban areas. Objectives To study the prevalence of H. pylori infection in primary school students in rural area and its contributing factors. Methods A cross-sectional study was performed in a rural primary school in Serang district, Banten, West Java. Serology of H. pylori was tested using Bio M pylori kit (Mataram, Indonesia). Results Forty two of 125 subjects (33.6%) had positive H. pylori serologies. Bivariate analysis found that the the family habit of eating together from one container increased the infection risk 5.93 times (95% Cl 3.07 to 11.43). Source of drinking water from common river increased the risk 9.88 times (95% CI 3.03 to 32.24). Bed and bedroom sharing increased the risk 1.55 times (95% CI 1.23 to 1.95) and 2.22 times (95% CI 1.65 to 2.99), respectively. Multivariate logistic regression analysis including all variables with P <0.25 showed that the most significant factor contributing to H. pylori infection is common river as family drinking water source (OR 24.97, 95% CI 3.9 to 159.76), followed by family habit of eating together from one container (OR 10.23, 95% CI 3.05 to 34.27), and bed or bedroom sharing (OR 9.48, 95% CI 2.4 7 to 36.38). Conclusion Prevalence of H. pylori infection in rural school students is 33.6%. There are significant associations between H. pylori infection and family habit of eating together from one container, bed sharing with other family members, and family drinking water source from common river.