Given the growing use of electric bidet toilets in Japan and other countries, we assessed the relationship between bidet toilet use and haemorrhoids or urogenital infections. Data were collected using a web-based longitudinal survey. In total, 10 305 subjects randomly selected from panels of a Japanese website research company for the baseline survey in 2013 were asked about their frequency of bidet toilet use and receipt of a doctor's diagnosis or subjective symptom of haemorrhoids and urogenital infections. One- and three-year follow-up surveys were performed in 2014 and 2016, respectively, and information on newly diagnosed/experienced outcomes occurring during the follow-up period were collected. Cumulative incidence of haemorrhoids and urogenital infections was not significantly increased by habitual use of a bidet toilet. In men, more habitual users reported subjective symptoms of irritated skin around the anus, which were newly experienced during follow-up than non-habitual users (adjusted risk ratio 1.36 (95% confidence interval 1.06–1.75)). Further studies are needed to confirm this relationship. Several of the outcomes were significantly more prevalent in habitual users, but these results were probably explained by reverse causation.