The purpose of this study was to evaluate and apply high-resolution three-dimensional phase contrast mapping for estimation of wall shear stress in vivo. A silicon pipe of 8 mm diameter with a 8.3 ml/s steady flow and the entrance of the carotid bifurcation in 10 young healthy volunteers aged 23.6 +/- 3.1 years was studied. Very high resolution three-dimensional and two-dimensional phase contrast mapping sequences with spatial resolutions of 0.31 x 0.31 x 1.5 mm(3) and 0.31 x 0.31 x 3 mm(3), respectively, were compared in vivo and in vitro. Wall shear stress was calculated using multi-sectored, three-dimensional paraboloid fitting. In comparison to the two-dimensional measurements, the three-dimensional method with only half the slice thickness gave higher signal-to-noise ratio and velocity-to-noise ratios both in vivo and in vitro. Wall shear stress derived from the three-dimensional velocity measurements did not differ from the two-dimensional velocity measurements either in vitro or in vivo. Mean wall shear stress was lowest and oscillatory shear index was highest at the outer wall, towards the carotid bifurcation. Three-dimensional velocity mapping increases resolution and image quality and allows estimation of wall shear stress patterns circumferentially and longitudinally in human arteries.