Background Peri-implantitis is a usual finding but estimates of its prevalence fluctuate very much. This may be due to the wide variety of disease definitions. This systematic review aims to estimate the overall prevalence of peri-implantitis and the effect of different study designs, function times and use of probing depth on prevalence rate. Methods Following electronic and manual searches of the literature published from January 2005 to December 2021, data were extracted from the studies fitting the study criteria. Fifty-seven articles were included in this study. Results Prevalence of peri-implantitis was 19.53% (95% CI 12.87–26.19) at the patient-level, and 12.53% (95% CI 11.67–13.39) at the implant-level and it remains highly variable even following restriction to the clinical case definition. The use of probing depth like diagnostic criteria affected the prevalence data. Conclusion The results indicate that it remains essential the identification of the diagnostic markers for more accurate disease classification.