ObjectivesLimited evidence is available regarding the financial relationships between gastroenterologists and pharmaceutical companies in Japan. This study analysed the magnitude, prevalence and trends of personal payments made by major pharmaceutical companies to board-certified gastroenterologists in Japan in recent years.DesignCross-sectional analysisSetting and participantsUsing payment data publicly disclosed by 92 major pharmaceutical companies, this study examined the non-research payments made to all board-certified gastroenterologists by the Japanese Society of Gastroenterology.Primary and secondary outcome measuresThe primary outcomes were payment amounts, the prevalence of gastroenterologists receiving payments, yearly trends in per-gastroenterologist payment values and the number of gastroenterologists with payments. Additionally, we evaluated the differences in payments among influential gastroenterologists, including clinical practice guideline authors, society board member gastroenterologists and other general gastroenterologists.ResultsApproximately 52.8% of all board-certified gastroenterologists received a total of US$89 151 253, entailing 134 249 payment contracts as the reimbursement for lecturing, consulting and writing, from 84 pharmaceutical companies between 2016 and 2019. The average and median payments per gastroenterologist were US$7670 (SD: US$26 842) and US$1533 (IQR: US$582–US$4781), respectively. The payment value per gastroenterologist did not significantly change during the study period, while the number of gastroenterologists with payments decreased by −1.01% (95% CI: −1.61% to −0.40%, p<0.001) annually. Board member gastroenterologists (median: US$132 777) and the guideline authoring gastroenterologists (median: US$106 069) received 29.9 times and 17.3 times higher payments, respectively, than general gastroenterologists (median: US$284).ConclusionMost gastroenterologists received personal payments from pharmaceutical companies, but only very few influential gastroenterologists with authority accepted substantial amounts in Japan. There should be transparent and rigorous management strategies for financial conflicts of interest among gastroenterologists working in influential positions.