This cross-sectional study aimed to evaluate the association between periodontitis and cardiovascular disease (CVD) by reviewing and discussing the role of the oral microbiome in periodontitis and CVD. This prospective cohort study used epidemiological data from the Korean Genome and Epidemiology Study from 2004 to 2016. We selected 9973 patients with periodontitis and 125,304 controls (non-periodontitis) from 173,209 participants and analyzed their medical histories to determine the relationship between cerebral stroke/ischemic heart disease and periodontitis. The participants were questioned about any previous history of hypertension, diabetes mellitus, hyperlipidemia, cerebral stroke (hemorrhagic or ischemic), ischemic heart disease (angina or myocardial infarction), and periodontitis. Their body mass index, smoking habit, alcohol intake, nutritional intake, and income were recorded. The Chi-square test, independent t-test, and two-tailed analyses were used for statistical analysis. The adjusted OR (aOR) of periodontitis for stroke was 1.35 (95% confidence interval (CI) = 1.16–1.57, p < 0.001). The aOR of periodontitis for ischemic heart disease was 1.34 (95% CI = 1.22–1.48, p < 0.001). We concluded that periodontitis was associated with CVD and may be a risk factor for CVD. However, further studies are required to determine the association between periodontal treatment and CVD.