Progress in modification of conventional coronary risk factors and lifestyle behavior reduced atherosclerotic coronary artery disease incidence, nonetheless it continues to be the leading cause of mortality in the world. It might be attributed to the defective risk stratifying and prevention strategy for coronary artery disease. Atherosclerotic coronary artery disease risk is estimated based on identifying and quantifying only traditional risk factors in current clinical settings, it does not consider non-traditional risk factors. In addition, most of prevailing therapies for atherosclerosis are targeted for traditional risk factors rather than atherosclerosis itself. It is desirable to have a methodology which can directly assess the activity of atherogenesis at each moment. Endothelial function is an integrated index of all atherogenic and atheroprotective factors present in an individual including non-traditional and heretofore unknown factors, and is reported to have additional predictive value for future cardiovascular events to traditional risk factors. Moreover, endothelial function has a pivotal role in all phases of atherosclerosis, from initiation to atherothrombotic complication, and is reversible at every phase, indicating that endothelial function-guided therapies might be effective and feasible in cardiovascular practice. Thus, the introduction of endothelial function testing into clinical practice might enable us to innovate individualized cardiovascular medicine. In this review, we summarize the current knowledge on the contribution of endothelial dysfunction to atherogenesis and review methods that assess endothelial function. Finally we focus on the effects of major anti-atherosclerotic disease therapies on endothelial function, and argue the possibility of non-invasive assessment of endothelial function aiming at individualized cardiovascular medicine.