Recent evidence is supporting the notion of a microbiological and immunological continuum on the gum-gut axis in health and disease. Therefore, the purpose of this study was to assess the prevalence and risk indicators of periodontitis in patients with Crohn's disease (CD) or ulcerative colitis (UC) compared to age- and sex-matched controls without inflammatory bowel disease (IBD). A total of 180 IBD (117 CD, 60 UC, 3 IBD-unclassified) and 180 healthy controls were compared for their periodontitis diagnosis (Centers for Disease Control and Prevention/American Academy of Periodontology [CDC/AAP] case definition) and full-mouth periodontal parameters. In addition, explorative logistic regression models were performed. Significantly more patients with IBD had moderate/severe periodontitis (85.6% vs. 65.6%, p<0.001) and severe periodontitis (36.7% vs. 25.6%, p<0.001) than controls. Differences were higher in the 35-50 and 51-65 age groups, without significant changes between CD and UC. IBD subjects presented chances ∼3.5 higher of having moderate/severe periodontitis (p<0.001). Significant variables associated with periodontitis in the whole sample were older age, presence of IBD, and higher full-mouth plaque scores, whereas in the IBD group they were male sex, IBD-associated surgery, and IBD duration and localization (pancolitis). Positive risk indicators for IBD were periodontitis severity and higher bleeding scores, while smoking was negatively associated with UC. Relevant associations between IBD and periodontitis were found, being modified by CD and UC clinical characteristics. Preventive and therapeutic strategies involving the gum-gut axis should be enforced in IBD patients.