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The burden of inflammatory bowel disease (IBD) hasn’t been reported in Iran. We aimed to estimate the prevalence and incidence of IBD and its trend in Iran at national and subnational level from 1990 to 2012. We conducted a systematic review of English and Persian databases about the epidemiology of IBD. We also collected outpatient data from 17 provinces of Iran using almost all public and private referral Gastroenterology clinics. prevalence and incidence rate was calculated at national and subnational levels. The Kriging method was used to extrapolate provinces with missing data and GPR model to calculate time trends of rates at subnational level. We found 16 case series, two population-based studies, and two review articles. We collected 11, 000 IBD cases from outpatient databases. Among them, 9, 269 (84. 26%) had ulcerative colitis (UC), 1, 646 (14. 96%) had Crohn’s disease (CD), and 85 had intermediate colitis (IC). A total of 5, 452 (49. 56%) patients were male. Mean age at diagnosis was 32. 80 years (CI: 13–61) for UC and 29. 98 years (CI: 11–58) for CD. Annual incidences of IBD, UC, and CD in 2012 were 3. 11, 2. 70, and 0. 41 per 100, 000 subjects respectively. prevalence of IBD, UC, and CD in 2012 were 40. 67, 35. 52, and 5. 03 per 100, 000 subjects respectively. The incidence of UC and CD showed a significant increase during the study period (P for trend< 0. 05). The incidence and prevalence of IBD are increasing in Iran. Establishing a national IBD registry seems necessary for comprehensive care of IBD patients in Iran.