Abstract In view of the epidemiological relevance of periodontal disease and chronic noncommunicable diseases, the study aimed to evaluate the relationship between them through subclinical indicators of systemic risk in a population group with healthy habits, including alcohol and tobacco abstinence. A complete periodontal examination of six sites per tooth was performed in a sample of 420 participants from the Advento study (Sao Paulo), submitted to anthropometric and laboratory evaluation. Periodontitis was defined and classified based on the Community Periodontal Index score 3 (periodontal pocket = 4-5 mm) and score 4 (periodontal pocket ≥ 6 mm). The prevalence of mild/moderate and severe periodontitis was 20% and 8.2%, respectively. Both categories of periodontal disease had significantly higher levels of triglycerides, C-reactive protein, calcium score, and calcium percentile, whereas blood glucose after tolerance test was significantly higher among people with severe periodontitis and HDL-c levels were lower (p < 0.05). Young adults with severe periodontitis had significantly higher prevalence of obesity, pre-diabetes, hypertension, and metabolic syndrome. Besides these conditions, the older adults with severe periodontitis had significantly higher prevalence of dyslipidemia and subclinical atherosclerosis. The group with periodontitis had also a higher coronary heart disease risk based on the PROCAM score (p < 0.05). The results indicated associations of periodontitis with several systemic indicators for chronic noncommunicable diseases, and highlighted the need for multiprofessional measures in the whole care of patients.