Background Inflammatory bowel disease (IBD) and periodontitis are chronic, progressive, inflammatory diseases with similarities in their respective pathogenesis, which involve a complex interplay between a dysbiotic microbiota and a dysregulated immune-inflammatory response. Periodontitis has been associated with an adverse impact on other inflammatory diseases and the general health. Whether presence of periodontitis is associated with IBD disease activity is uncertain. Methods A questionnaire-based survey was conducted in Denmark. A total of 1,093 patients with IBD, i.e., 527 patients with Crohn’s disease (CD) and 566 patients with Ulcerative colitis (UC), answered the questionnaire. The survey included questions on social demographics, oral health, as well as IBD-related characteristics. Oral health was assessed by the number of teeth, the state of teeth and gums, and the Periodontal Screening Score (PESS) which is a validated instrument to screen for severe periodontitis. Disease activity in patients with UC and CD was assessed by the Simple Clinical Colitis Index (SCCAI) and the Harvey & Bradshaw’s Activity Index (HBI), respectively. Disease related disability was assessed by the Inflammatory bowel disease disability index (IBD-DI). Univariate and multivariate statistical analyses were performed to assess each variable. Results Patients with CD reported significantly fewer remaining teeth (p=0.004) and poorer state of teeth and gums (p=0.001) in comparison to patients with UC. Irrespective of IBD disease subtype, patients with a reduced number of teeth scored significantly higher on the IBD disability index (p=0.001) and reported an increased disease activity in the last 12 months (p=0.001). Patients with self-reported severe periodontitis scored significantly higher on the IBD disability index (p=0.041) and reported an increased disease activity in the last 12 months (p=0.001). For patients with UC, self-reported severe periodontitis was associated with a higher SCCAI score (p=0.031). Likewise, patients with CD who had a reduced number of teeth scored significantly higher on the HBI (p=0.017). Conclusion Periodontitis was significantly associated with increased IBD disease activity as well as increased IBD disease related disability. CD patients had significantly poorer oral health compared with UC patients. Our results highlight a need for an increased focus on oral health in patients with IBD.