To investigate the influence of rehabilitation characteristics in the incidence of peri-implant pathology (P-iP). A total of 1350 patients (270 with P-iP matched for age, gender, and time of follow-up with 1080 controls without P-iP) rehabilitated with dental implants were included. The effect of the independent variables [Implant length in millimeters (IL); implant diameter in millimeters; implant surface (IS); presence of cantilevers; implant:crown ratio (ICR), type of abutment (TA); abutment height; fracture of prosthetic components (FPCs); type of prosthetic reconstruction (TPR); type of material used in the prosthesis (TMUP); loosening of prosthetic components (LPCs); and passive misfit (PM) diagnosed within the previous year] was evaluated through bivariate analysis (chi-square), with level of significance of 5%. Crude odds ratios (OR) with 95% confidence intervals and the attributable fraction (AF) were calculated for the independent variables individually identified as factors associated with the incidence of peri-implant pathology. The following variables were identified as risk factors: machined IS (p = 0.015; OR = 1.46), 17° TA (p = 0.000; OR = 3.06), completely edentulous TPR (p = 0.000; OR = 2.49), TMUP (p = 0.000; metal-acrylic OR = 2.29; acrylic OR = 4.90; metal-ceramic OR = 8.43), 1:1 ICR (p = 0.002; OR = 1.54), FPC (p = 0.000; OR = 3.01), LPC (p = 0.000; OR = 4.15), and PM (p = 0.002; OR = 20.36). The attributable fraction rendered the following theoretical potential reductions in the cases if the exposure to the variables was removed: IS (31.5%), TA (67.3%), TMUP (5.4% to 73.3%), ICR (35%), FPC (66.8%), LPC (73.8%), and PM (95.1%). Within the limitations of this study, machined implant surfaces, 17° abutments, completely edentulous reconstructions, the type of metal used in the prosthesis, 1:1 implant:crown ratio, fracture of prosthetic components, loosening of prosthetic components, and passive misfit emerged as risk factors for the incidence of P-iP. Eliminating the exposure to these variables would, in theory, result in a significant reduction in the incidence of P-iP.