Endothelial cells are actively involved in various aspects of vascular biology and different stages of atherosclerosis. Endothelial function is increasingly used as an important outcome measure in cardiovascular research. Endothelial progenitor cells (EPCs) are closely linked to endothelial function, and their biomarkers have received much attention. EPCs may not only serve as a pool of progenitor cells and possess the capacity to repair the damaged vasculature, but also act as potent effectors in systemic inflammation, suggesting that EPCs may play a critical role in maintaining endothelial function and the progression of cardiovascular disease (CVD). Emerging evidence shows an association of periodontal infections (gingivitis and periodontitis) with endothelial dysfunction, while the relevant mechanisms remain unknown. Our recent finding of the association of periodontitis with EPCs warrants their utilization as additional biomarkers in future studies on periodontal medicine. This review starts with a brief account on the current understanding of the nature of periodontal infections and their link with systemic inflammation and endothelial dysfunction. The paper also provides an update on endothelial biology and function as well as the novel biomarkers of EPCs and concludes with clinical studies on periodontal diseases and CVD.