Background/purpose Inflammatory bowel disease (IBD), comprised Crohn's disease and ulcerative colitis, is a mucosal immune response that affects gastroenterological tract. The association between IBD and periodontitis was inconclusive. In this study, we aimed to investigate the association between IBD and periodontitis by using a register-based dataset. Materials and methods The dataset conducting in this retrospective cohort study was obtained from the National Health Insurance Research database (NHIRD) in Taiwan. For IBD group, conditionally selected control subjects were matched in 1:4 ratio from general population. The risk of periodontitis among IBD group comparing with non-IBD group was calculated by multivariable Cox proportional hazards model. Results In IBD cohort, 27 IBD patients (7 Crohn's disease and 20 ulcerative colitis) with catastrophic illness registry were identified. 108 controls were selected as non-IBD cohort. The median follow-up period was 3.00 years in the IBD group and 3.15 years in the non-IBD group. The cumulative incidence of IBD was 4.32 per 100,000 persons. After adjusting for several confounding factors, IBD group had higher risk for developing periodontitis than non-IBD group (adjusted HR: 1.82; 95% CI: 1.09–3.03). To further stratification with subtype, Crohn's disease group had significantly higher risk of periodontitis (adjusted HR: 3.95; 95% CI: 1.59–9.82). Conclusions Taken together, this retrospective cohort study showed that patients with IBD increase risk of having periodontitis comparing with non-IBD group, especially in Crohn's disease subgroup.