Background Although the coronary arteries are equally exposed to systemic risk factors, coronary atherosclerosis is focal and eccentric, and each lesion evolves in an independent manner. Variations in shear stress elicit markedly different humoral, metabolic, and structural responses in endothelial cells. Areas of low shear stress promote atherosclerosis, whereas areas of high shear stress prevent atherosclerosis. Characterization of the shear stresses affecting coronary arteries in humans in vivo may permit prediction of progression of coronary disease, prediction of which plaques might become vulnerable to rupture, and prediction of sites of restenosis after percutaneous coronary intervention. Methods To determine endothelial shear stress, the 3-dimensional anatomy of a segment of the right coronary artery was determined immediately after directional atherectomy by use of a combination of intracoronary ultrasound and biplane coronary angiography. The geometry of the segment was represented in curvilinear coordinates and a computational fluid dynamics technique was used to investigate the detailed phasic velocity profile and shear stress distribution. The results were analyzed with several conventional indicators and one novel indicator of disturbed flow. Results Our methodology identified areas of minor flow reversals, significant swirling, and large variations of local velocity and shear stress—temporally, axially, and cirumferentially—within the artery, even in the absence of significant luminal obstruction. Conclusions We have described a system that permits, for the first time, the in vivo determination of pulsatile local velocity patterns and endothelial shear stress in the human coronary arteries. The flow phenomena exhibit characteristics consistent with the focal nature of atherogenesis and restenosis. (Am Heart J 2002;143:931-9.)