Background The relationship between bile acid reflux into the stomach and the risk of atrophic gastritis and intestinal metaplasia is still not well understood. Towards obtaining a better understanding, concentrations of bile acids were measured. Patients and Methods This study was carried out with the participation of 14 facilities in J apan, and 2283 samples were collected. The subjects with bile acid concentrations equal to or higher than the limit of detection were divided into four groups of equal size (group A : 0–25%, group B : 26–50%, group C : 51–75%, and group D : 76–100%). Thus, including the control group, there were five groups in total. The odds that the control group would develop atrophic gastritis and intestinal metaplasia was set as 1,and the odds ratios ( OR ) in groups A , B , C and D were calculated based on the odds in the control group. Results Regarding the development of atrophic gastritis, no increased risk was observed in either the H elicobacter pylori ( H . pylori )‐positive or ‐negative cases. The OR for the development of intestinal metaplasia were significantly higher, for both cases with and without H . pylori infection, in group D . Conclusion High concentrations of bile acid seem to be associated with an elevated risk of intestinal metaplasia.