Background Periodontitis is one of candidates associated with elevated levels of C-reactive protein (CRP) and other inflammatory biomarkers. Epidemiologic studies have shown that periodontitis is associated with endothelial dysfunction, atherosclerosis, and an increased risk of coronary heart disease and stroke. We aimed to investigate the relation between periodontitis and the inflammation of the carotid artery. Method We observed 86 patients with clinical diagnosis of periodontitis and 42 subjects without it. All subjects underwent F-18 fluorodeoxyglucose (FDG) positron emission tomography/ computed tomography and were evaluated for the level of inflammation using the maximum standardized uptake value (max SUV) of FDG in the right carotid artery and the dental region. Results The patients with periodontitis showed significantly higher SUV of dental region (2.8짹0.4 vs. 1.2짹0.7, p<0.001) and right carotid artery (2.5짹0.4 vs. 0.8짹0.7, p<0.001) and high-sensitivity CRP (hsCRP) (2.18짹3.10 mg/l vs. 1.20짹1.12 mg/l, p=0.014) than control. The correlation of dental SUV was very high with carotid artery SUV (r=0.851, p<0.001) but modest with hsCRP (r=0.179, p=0.51). The hsCRP showed no correlation with carotid artery SUV (r=0.096, p=0.301). In multiple linear regression analysis, carotid SUV was significantly associated with periodontitis (R2=0.730, p<0.001) or dental SUV (R2=0.763, p<0.001) independent of age, sex, hsCRP or other covariates. Conclusion Independent of systemic inflammation, these data suggest that periodontitis per se and its degree of inflammation appear to be closely associated with vascular inflammation, a crucial mechanism of the development, progression and vulnerability of atherosclerotic plaque.