Although multiple combinations of weather variability may contribute to an increased incidence of infectious gastrointestinal disease, few studies have investigated the association between weather variability and cases of infectious gastroenteritis. We acquired data for infectious gastroenteritis cases and weather variability in Fukuoka, Japan, from 1999 to 2007 and used time-series analysis to assess the effects of weather variability on infectious gastroenteritis cases, adjusting for confounding factors. In total, 422 176 infectious gastroenteritis cases were reported during the 9-year study period. The weekly number of infectious gastroenteritis cases increased by 7·7% (95% CI 4·6–10·8) for every 1°C increase in the average temperature and by 2·3% (95% CI 1·4–3·1) for every 1% decrease in relative humidity. From 1999 to 2007, infectious gastroenteritis cases increased significantly with increased average temperature and decreased relative humidity in Fukuoka, Japan.