Objectives: Due to the inconsistent definitions, reporting methods and study characteristics, prevalences of periimplant diseases significantly varied in studies. This study aimed to systematically analyze implant-based and subject-based prevalences of peri-implant diseases and assess clinical variables potentially affecting the prevalence. Sources: Electronic search of studies was conducted using MEDLINE (PubMed), EMBASE and Web of Science. Publication screening, data extraction, and quality assessment were performed. Study selection: Clinical studies having an at least average three-year follow-up period were selected. The numbers of subjects and implants in the studies had to be equal to or more than thirty. Data: Forty seven studies were selected and prevalences of peri-implant diseases were analyzed. Since heterogeneity existed in each outcome (I-2 = 94.7, 95.7, 95.3, and 99.3 for implant-based and subject-based peri-implantitis and peri-implant mucositis, respectively), the random-effects model based on the DerSimonian and Laird method, which incorporate an estimate of heterogeneity in the weighting, was applied to obtain the pooled prevalence. Weighted mean implant-based and subject-based peri-implantitis prevalences were 9.25% (95% Confidence Interval (CI): [7.57, 10.93]) and 19.83% (CI [15.38, 24.27]) respectively. Weighted mean implant-based and subject-based peri-implant mucositis prevalences were 29.48% (CI: [22.65, 36.32]) and 46.83% (CI: [38.30, 55.36]) respectively. Functional time and implant to subject ratio were associated with subject-based peri-implantitis prevalence, but not peri-implant mucositis prevalences. Conclusions: Peri-implant diseases were prevalent and prevalence of peri-implantitis increased over time. Prevalences of peri-implantitis and peri-implant mucositis might not be highly associated since the prevalences were influenced by distinct variables. The results should be carefully interpreted because of data heterogeneity.