Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease. In small studies, inflammatory bowel disease has been associated with the increased prevalence of HS, but the data on the concurrence of inflammatory bowel disease in patients with HS are limited. We therefore investigated the prevalence and risk of inflammatory bowel disease in patients with HS compared with the general population. The study linked all Danish individuals aged ≥18 years in nationwide registers. Adjusted odds ratios and adjusted hazard ratios were estimated by logistic regression and Cox regression, respectively. The study comprised 7,732 patients with HS and 4,354,137 subjects from the general population. The prevalence (HS vs. general population) was 0.8% and 0.3% (odds ratio 2.04; 1.59–2.62) for Crohn's disease and 1.3% and 0.7% (odds ratio 1.75; 1.44–2.13) for ulcerative colitis. The risk of new-onset Crohn's disease (hazard ratio 2.19; 1.44–3.34) and ulcerative colitis (hazard ratio 1.63; 1.18–2.27) was significantly increased among patients with HS. In conclusion, HS was significantly associated with the presence and risk of new-onset inflammatory bowel disease, although the prevalence remained low. Gastrointestinal complaints in patients with HS should warrant further clinical examination.