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PURPOSE To evaluate the prevalence of peri-implant diseases in a university patient sample and to analyse possible risk variables associated with their occurrence. MATERIALS AND METHODS One hundred and eighty-six patients with 597 implants were examined clinically and radiographically. The mean period of function was 5.5 years (range 1 to 16.5 years). A subgroup analysis was performed for implants with a minimum function time of 5 years. Outcome measures were implant failures, prevalence and risk indicators of peri-implant diseases. In order to identify statistically significant risk indicators of peri-implant mucositis and peri-implantitis multi-level logistic regression models were constructed. RESULTS The prevalence of peri-implantitis and peri-implant mucositis on patient levels were 12.9% (13.3% for ≥ 5 years) and 64.5% (64.4% for ≥ 5 years), respectively. Multi-level analysis showed that a high plaque score (OR = 1.365; 95% CI: 1.18 to 1.57, P < 0.001) was a risk indicator for periimplant mucositis, while augmentation of the hard or soft tissue at implant sites had a protective effect (OR = 0.878 95% CI: 0.79 to 0.97, P = 0.01). It was also shown that the odds ratio for having peri-implant mucositis increased with the increase of plaque score in a dose-dependent manner. With respect to peri-implantitis, loss of the last tooth due to periodontitis (OR = 1.063; 95% CI: 1.00 to 1.12, P = 0.03) and location of the implants in the maxilla (OR = 1.052, 95% CI: 1.00 to 1.09, P = 0.02) were identified as statistically significant risk indicators. CONCLUSIONS Within the limitations of this study, the history of periodontal disease was the most significant risk indicator for peri-implantitis and the level of oral hygiene was significantly associated with peri-implant mucositis.