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Objective The aim was to compare the inflammatory response in peri-implant mucosa between patients with peri-implantitis (PP-group) and patients with healthy peri-implant tissues (HP-group). Materials and methods Two fragments of peri-implant mucosa of 18 patients were collected and serial sections were performed for histological and immunohistochemical analysis. Results When compared with HP-group, PP-group showed higher immunostained cell density for TGF-β, IL-17 and CD31, beyond greater density of red cells, leukocytes, mast cells chymase (MCC) and mast cell tryptase (MCT). HP-group patients showed higher IL-13 expression and increased amount of collagen fibres when compared with PP-group. In PP-group there was significant positive correlation between MCT density and density of blood vessels immunostained, and between MCC density and density of blood vessels immunostained. There was significant negative correlation between the IL-17 density and collagen percentage. Conclusions This study demonstrated that in patients with peri-implantitis there was higher of TGF-β and IL-17, indicating that these cytokines are directly involved in the inflammatory process. Thus, understanding the influence of cytokines in the peri-implantitis installation, new therapies could be developed in order to inhibit the synthesis of IL-17 and induce synthesis of IL-13 in peri-implant tissue, contributing to increase the longevity of the implant.