Atherosclerosis, which is a degenerative vascular disease, is believed to occur in the blood vessels due to deposition of cholesterol or low density lipoprotein (LDL). Atherosclerotic lumen narrowing causes reduction of blood flow due to hemodynamic features. Several hypothetical theories related to the hemodynamic effects have been reported : high shear stress theory, low shear stress theory, high shear stress gradient theory, flow separation and turbulence theory, and high pressure theory. However, no one theory clearly explains, the causes of atherosclerosis. The objective of the present study was to investigate the mechanism of the generation of atherosclerosis. In the study, the database of Korean carotid and coronary arteries for geometrical and hemodynamic clinical data was established. The atherosclerotic sites were predicted by the computer simulations. The results of the computer simulation were compared with the in vivo experimental results, and then the pathogenesis of atherosclerosis by using the clinical data and several hypothetical theories were investigated. From the investigation, it was concluded carefully that the mechanism of the generation of atherosclerosis was related to the hemodynamic effects such as flow separation and oscillatory wall shear stress on the vessel walls.