Objective: To evaluate the expression of the cytokines IFN-γ, IL-1β, IL-4, IL-6, IL-10, IL-21, IL-22, IL-23, IL-25, IL-31, IL-33, IL-17A, IL-17F, sCD40L, and TNF-α in gingival tissue and intestinal mucosa of patients having both periodontitis and inflammatory bowel disease (IBD) and assess how they cluster in both tissues. Methods: This cross-sectional study selected 28 patients with periodontitis (18 with Crohn's disease and 10 with ulcerative colitis) from the IBD gastroenterology outpatient clinic at the Pedro Ernesto University Hospital. Patients were assessed using questionnaire, medical chart check and periodontal examination. Gingival and intestinal biopsies were collected and homogenized using a cell disruptor. Cytokines expression was evaluated through multiplex technology. Cluster analysis was performed based on cytokinés correlation strength and presented in dendrograms. Results: Crohn's disease and ulcerative colitis patients exhibited no significant difference between them in cytokine levels (p > 0.05), so they were analysed together. Significantly higher levels of IL-17A, IL-17F, IL-22, IL-25, IL-33, IL-10, and INF-γ were found in gingival tissues in comparison with intestinal mucosa (p < 0.05). In gingival tissue, cytokines formed the following clusters: IL-25/IL-10/IL-33 (r = 0.775), IL-22/IL-23/IL-6 (r = 0.681) and IL-6/IL-25/IL-33/IL-10 (r = 0.660). In intestinal mucosa, the following clusters were formed: IL-6/IL-21/IL-10 (r = 0.880), IL-17A/IL-6/IL-21/IL-10 (r = 0.826), IL-I7F/IL-33/IL-25 (r = 0.813) and IL-23/IL-2/IL-17A/IL-6/IL-21/IL-10 (r = 0.785). Conclusion: Expression of IL-17A, IL-17F, IL-22, IL-25, IL-33, IL-10, and INF-γ was significantly increased in gingival tissue in comparison with intestinal mucosa of patients with periodontitis and IBD. The cytokine clustering pattern was different in gingival and intestinal tissues.