The mode of transmission of Helicobacter pylori, a bacterium causing gastric cancer and peptic ulcer disease, is unknown although waterborne transmission is a likely pathway. This study investigated the hypothesis that access to treated water and a sanitary sewerage system reduces the H. pylori incidence rate, using data from 472 participants in a cohort study that followed children in Juarez, Mexico, and El Paso, Texas, from April 1998, with caretaker interviews and the urea breath test for detecting H. pylori infection at target intervals of six months from birth through 24 months of age. The unadjusted hazard ratio comparing bottled/vending machine water to a municipal water supply was 0.71 (95% confidence interval (CI): 0.50, 1.01) and comparing a municipal sewer connection to a septic tank or cesspool, 0.85 (95% CI: 0.60, 1.20). After adjustment for maternal education and country, the hazard ratios decreased slightly to 0.70 (95% confidence interval: 0.49, 1.00) and 0.77 (95% confidence interval: 0.50, 1.21), respectively. These results provide moderate support for potential waterborne transmission of H. pylori.