The integrity and functional activity of the endothelial monolayer play a crucial role in the prevention of atherosclerosis. Increasing evidence suggests that risk factors for coronary artery disease increase endothelial cell apoptosis and lead to a disturbance in the endothelial monolayer. Recent insights suggest that the injured endothelial monolayer is regenerated by circulating bone marrow derived endothelial progenitor cells, which accelerates reendothelialization and limits atherosclerotic lesion formation. However, risk factors for coronary artery disease such as age and diabetes reduce the number and functional activity of these circulating endothelial progenitor cells, thus limiting the regenerative capacity. The impairment of stem/progenitor cells by risk factors may contribute to atherogenesis and atherosclerotic disease progression. We discuss this novel concept of endothelial regeneration and highlight possible novel strategies to interfere with the balance of injury and repair mechanisms.