Atherosclerosis, an inflammatory process that selectively affects arteries, is highly prevalent in human. Thrombo-occlusive complications of atherosclerosis, including stroke and myocardial infarction, are becoming major causes of morbidity and mortality in the industrialized world. Atherosclerosis develops in response to local endothelial injuries. Endothelial dysfunction and cell loss are prominent features in atherosclerosis. Restoring the endothelial lining to normal is critical for slowing or reversing the progression of atherosclerosis. Increasing data suggest that endothelial progenitor cells (EPCs) play a significant role in reendothelialization of the injured blood vessels. This review focuses on the effects of EPC mobilization and transfusion in the condition of atherosclerosis. The aim of the review is to provide an update on the progress in this research field, highlight the role of EPCs in atherosclerosis and discuss the possible mechanisms and potential risks of progenitor cell-based therapy in atherosclerosis.