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The major transmission route of Helicobacter pylori remains unclear. In this study, we examined H. pylori in the environmental waters in Japan.A total of 24 water samples were collected from the upper, middle and downstream reaches of four Japanese rivers. Helicobacter pylori-specific DNA was examined using nested PCR. In addition, 224 children who lived near one river were studied by the stool antigen test for H. pylori prevalence. Helicobacter pylori DNA was detected in the water from the middle and downstream reaches of all four rivers, but not in the upper reaches. Helicobacter pylori was not found in cultured water samples with positive PCR results. Helicobacter pylori prevalence in the children examined was 9.8% for those living near the middle reaches and 23.8% nearby downstream, both of which were higher than the value in an area distant from the river (0%) (both, P < 0.01).Difference in H. pylori prevalence in the children may be related to the presence of H. pylori in the river. The results of this study showed that H. pylori DNA is frequently present in river water from the middle and downstream reaches in which the human biosphere is embedded.It is suggested that river water in the natural environment could be a risk factor for H. pylori transmission.