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Hirschsprung disease (HSCR) has previously been associated with inflammatory bowel disease (IBD). There are no data to show how common this association is. The aim of the present study was to assess the risk of IBD in individuals with HSCR in a population-based cohort.This was a nationwide, population-based cohort study. The study exposure was HSCR and the study outcome was IBD. The cohort included all individuals with HSCR registered in the Swedish National Patient Register between 1964 and 2013 and 10 age- and sex-matched controls per patient, randomly selected from the Swedish Population Register. Individuals with IBD were identified in the Swedish National Patient Register. Data were validated by checking for relevant surgical procedures, and, or prescription of drugs for IBD registered in the Swedish Drug Registry.The cohort comprised 739 individuals with HSCR (565 boys) and 7390 controls (5650 boys). The median age at diagnosis of IBD was not different between the groups; 19 years (5–34) versus 21 years (7–37), P = 0.21. Twenty of the 739 individuals with HSCR and 41 of the 7390 controls had IBD, odds ratio 4.99, and 95% confidence interval 2.85 to 8.45. In the exposed group, 15 individuals had Crohn disease and 5 ulcerative colitis at their latest admission compared to 18 individuals with Crohn disease and 23 with ulcerative colitis in the unexposed group, P = 0.030.There is an increased risk of IBD in patients with HSCR, which should be considered in clinical practice.