Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease. In small studies, inflammatory bowel disease (IBD) has been associated with increased prevalence of HS, but data on the concurrence of IBD in patients with HS is limited. We therefore investigated the prevalence and risk of IBD in patients with HS compared with the general population. The study linked all Danish individuals ≥18 years in nationwide registers. Adjusted odds ratios (OR) and adjusted hazard ratios (HRs) 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% (OR 2.04; 1.59-2.62) for CD and 1.3% and 0.7% (OR 1.75; 1.44-2.13) for UC. The risk of new-onset CD (HR 2.19; 1.44-3.34) and UC (HR 1.63; 1.18-2.27) was significantly increased among patients with HS. In conclusion, HS was significantly associated with presence and risk of new-onset IBD, although the prevalence remained low. Gastrointestinal complaints in patients with HS should warrant further clinical examination.