BACKGROUND: Almost a quarter century has passed since the first nationwide survey on ulcerative colitis (UC) and Crohn's disease (CD) was conducted in Japan. In this study, we used a nationwide survey to estimate the number of patients and prevalence of these diseases in Japan in 2014. METHODS: We conducted a mail-based survey targeting hospitals to estimate the annual numbers of patients with UC and CD in 2014. Respondents were asked to report the numbers of patients who met specific diagnostic criteria for these two conditions. A stratified random sampling method was used, and a total of 3712 departments (internal medicine, surgery, pediatrics, and pediatric surgery) were selected for analysis. The overall and sex-specific annual numbers of UC and CD patients were estimated. The corresponding prevalence rates per 100,000 population were calculated by dividing the number of patients with each disease by the mid-year population of Japan in 2014. RESULTS: The overall survey response rate was 56.7% (2016 departments). The estimated numbers of patients with UC and CD were 219,685 (95% confidence interval: 183,968-255,403) and 70,700 (56,702-84,699), respectively. The annual prevalence rates of UC and CD per 100,000 population were 172.9 (men: 192.3; women: 154.5) and 55.6 (men: 79.5; women: 33.1), respectively. These numbers are almost tenfold increase in comparing the previous survey (22,300 in UC and 7,400 in CD). The male-to-female ratios were 1.24 for UC and 2.40 for CD, and the UC-to-CD ratio was 3.11. CONCLUSIONS: The prevalence of UC and CD in Japan has risen substantially over the past two decades, and their disease burden requires further examination.