The aim of this study was to evaluate the prevalence of peri-implant disease and analyze risk indicators in Japanese subjects with ≥3years of implant function. Five hundred and forty-three subjects treated with 1,613 implants were evaluated. Information was collected about the patients' physical and dental history, as well as implant details. Peri-implant evaluation included probing depth, bleeding on probing (BoP), suppuration (Sup), and keratinized tissue width. Bone loss was calculated from intra-oral radiographs taken after 1year and more than 3years of function. Implants were classified into three groups: healthy, peri-implant mucositis (BoP without bone loss), and peri-implantitis (BoP and/or Sup with bone loss >1mm). These data were analyzed by multivariable multinomial logistic regression. The prevalence of peri-implant mucositis and peri-implantitis at the subject level was 23.9% and 15.8%, respectively. An association was found between peri-implant mucositis and plaque control record (PCR) >20% and keratinized tissue width <2mm. Peri-implantitis was associated with PCR >20%, smoking, insertion in the maxilla, and keratinized tissue width <2mm. Within the limitations of this study, the prevalence of peri-implant diseases was elucidated in a Japanese population. Peri-implant mucositis was associated with poor oral hygiene and less keratinized tissue. Poor oral hygiene, smoking, insertion in the maxilla, and less keratinized tissue were risk indicators for peri-implantitis.