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Peri-implantitis is an inflammatory disease affecting soft and hard tissues surrounding dental implants. As the global number of individuals that undergo restorative therapy through dental implants increases, peri-implantitis is considered as a major and growing problem in dentistry. A randomly selected sample of 588 patients who all had received implant-supported therapy 9 y earlier was clinically and radiographically examined. Prevalence of peri-implantitis was assessed and risk indicators were identified by multilevel regression analysis. Forty-five percent of all patients presented with peri-implantitis (bleeding on probing/suppuration and bone loss >0.5 mm). Moderate/severe peri-implantitis (bleeding on probing/suppuration and bone loss >2 mm) was diagnosed in 14.5%. Patients with periodontitis and with ≥4 implants, as well as implants of certain brands and prosthetic therapy delivered by general practitioners, exhibited higher odds ratios for moderate/severe peri-implantitis. Similarly, higher odds ratios were identified for implants installed in the mandible and with crown restoration margins positioned ≤1.5 mm from the crestal bone at baseline. It is suggested that peri-implantitis is a common condition and that several patient- and implant-related factors influence the risk for moderate/severe peri-implantitis (ClinicalTrials.gov NCT01825772).