Retrospectively, we assessed the likelihood that peri-implantitis was associated with a history of systemic disease, periodontitis, and smoking habits. Methods: Data on probing pocket depth (PPD), bleeding on probing (BOP), and radiographic bone levels were obtained from individuals with dental implants. Peri-implantitis was defined as described by Sanz & Chapple 2012. Control individuals had healthy conditions or peri-implant mucositis. Information on past history of periodontitis, systemic diseases, and on smoking habits was obtained. Results: One hundred and seventy-two individuals had peri-implantitis (mean age: 68.2 years, SD ± 8.7), and 98 individuals (mean age: 44.7 years, SD ± 15.9) had implant health/peri-implant mucositis. The mean difference in bone level at implants between groups was 3.5 mm (SE mean ± 0.4, 95% CI: 2.8, 4.3, P < 0.001). A history of cardiovascular disease was found in 27.3% of individuals with peri-implantitis and in 3.0% of individuals in the implant health/peri-implant mucositis group. When adjusting for age, smoking, and gender, odds ratio (OR) of having peri-implantitis and a history of cardiovascular disease was 8.7 (95% CI: 1.9, 40.3 P < 0.006), and odds ratio of having a history of periodontitis was 4.5 (95% CI 2.1, 9.7, P < 0.001). Smoking or gender did not significantly contribute to the outcome. Conclusions: In relation to a diagnosis of peri-implantitis, a high likelihood of comorbidity was expressed by a history of periodontitis and a history of cardiovascular disease.