We developed a system for measuring the wall shear stress (WSS) in blood vessels using magnetic resonance imaging (MRI) and computational fluid dynamics (CFD). The time-dependent velocity at the center of the blood vessel was measured by phase-contrast MRI and was approximated by finite Fourier series, which was used for generating the velocity profile at the inlet for the boundary condition to the CFD method. To validate the CFD method, we compared the WSS obtained by the CFD method with the theoretical value in a straight cylinder with vari ous radii for both steady and pulsatile flows. We also investigated the dependence of the WSS on the inlet velocity profile incorporated into the CFD method. For steady flow, there was a good agreement between the WSS obtained by the CFD method and the theoretical value. For pulsatile flow, there was a relatively good agreement between them when the radius of the cylinder was 2.5 mm and the inlet velocity profile was given by the Womersley solution for fully developed pulsatile flow in a straight circular cylinder. When the radius of the cylinder was 5 mm and/or the inlet velocity profile was assumed to be parabolic, large differences were observed between them, suggesting that the assumption of fully developed flow does not hold true in these cases. In human studies, the vortex due to the secondary blood flow in the carotid arterial sinus was clearly observed. The WSS in the bifurcation was the highest, while that in the carotid arterial sinus was the smallest. In conclusion, the system presented here appears to be useful for measuring the WSS in blood vessels and for analyzing the cause and/or extent of atherosclerosis, and our results suggest that the inlet velocity profile should be carefully considered.