Background: The aim of this cross-sectional study was (1) to determine the prevalence of peri-implant mucositis and peri-implantitis and (2) to reveal the risk indicators associated with peri-implant diseases. The second point was to investigate the role of keratinized mucosa on peri-implant health. Materials and methods: Three hundred and eighty-two subjects who were treated with 1415 dental implants between 2011-2017 were clinically evaluated. Patients' medical and dental history, as well as implant details, were recorded. Periimplant examination included probing pocket depth (PPD), bleeding on probing (BoP), plaque index (PI), gingival index (GI), and keratinized tissue width. Furthermore, the patient (sex, age, and smoking) and implant/prosthesis-related factors (surface characteristic, time in function, design of prosthesis etc.) were evaluated. Implants were classified into three groups: healthy, peri-implant mucositis, and peri-implantitis. Uni-and multi-variate regression analyses were utilized for statistics. Results: 41.1% (n = 157) and 36.9% (n = 84) of patients had mucositis and peri-implantitis, respectively. 53.6% (n = 758) of implants (95%CI 80.2-90.4) had mucositis, and 21.7% (n = 307) had peri-implantitis. Patients with a maintenance < 2/year (OR = 2.576), having periodontitis (OR = 3.342) and higher PI (OR = 3.046) had significant associations with the development of peri-implant mucositis. Significant ORs were determined for peri-implantitis with patients having maintenance < 2/year (OR = 2.048), having number of implants ≥ 4 (OR = 2.103), diagnosed with periodontitis (OR = 3.295), and higher PI (OR = 7.055). Keratinized tissue width < 2 mm (ORs = 5389/8.013), PPD (ORs = 1.570/8.338), PI (ORs = 6.726/5.205), and BoP (ORs = 3.645/4.353) independent variables were significantly associated with both peri-implant mucositis and peri-implantitis at implant level, respectively. Conclusions: Within the limits of this study, the prevalence of mucositis and peri-implantitis was shown to be high in Turkish population. Furthermore, increased risk for peri-implantitis was identified in patients having maintenance < 2/year, presence of periodontitis, poor plaque control, and having number of implants ≥ 4. Less keratinized tissue (< 2 mm), PPD, and BoP were also risk indicators for peri-implantitis development.