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The link between atherosclerosis and wall shear stress (WSS) has lead to considerable interest in the in vivo estimation of WSS. Both magnetic resonance imaging (MRI) and three-dimensional ultrasound (3DUS) are capable of providing the anatomical and flow data required for subject-specific computational fluid dynamics (CFD) simulations. This study compares, for the first time, predicted 3D flow patterns based on black blood MRI and 3DUS. Velocity fields in the carotid arteries of nine subjects have been reconstructed, and the haemodynamic wall parameters WSS, oscillatory shear index (OSI), WSS gradients (WSSG) and angle gradients (WSSAG) were computed and compared. There was a good qualitative agreement between results derived from MRI and 3DUS, embodied by a strong linear correlation between the patched representations of the haemodynamic wall parameters. The root-mean-square error between haemodynamic wall parameters was comparable to the range of the expected variability of each imaging technique (WSS: 0.411 N/m; OSI: 0.048; temporal WSSG: 2.29 N/(s.m2); spatial WSSG: 150 N/m3; WSSAG: 87.6 rad/m). In conclusion, MRI and 3DUS are comparable techniques for combining with CFD in the carotid artery. The relatively high cost of MRI favour 3DUS to MRI for future haemodynamic studies of superficial arteries.