Purpose To evaluate differences in carotid atherosclerosis measured using magnetic resonance imaging (MRI) and three‐dimensional ultrasound (3DUS). Materials and Methods Ten subject volunteers underwent carotid 3DUS and MRI (multislice black blood fast spin echo, T1‐weighted contrast, double inversion recovery, 0.5 mm in‐plane resolution, 2 mm slice, 3.0 T) within 1 hour. 3DUS and MR images were manually segmented by two observers providing vessel wall and lumen contours for quantification of vessel wall volume (VWV) and generation of carotid thickness maps. Results MRI VWV (1040 ± 210 mm3) and 3DUS VWV (540 ± 110 mm3) were significantly different (P < 0.0001). When normalized for the estimated adventitia volume, mean MRI VWV decreased 240 ± 50 mm3 and was significantly different from 3DUS VWV (P < 0.001). Two‐dimensional carotid maps showed qualitative evidence of regional differences in the plaque and vessel wall thickness between MR and 3DUS in all subjects. Power Doppler US confirmed that heterogeneity in the common carotid artery in all patients resulted from apparent flow disturbances, not atherosclerotic plaque. Conclusion MRI and 3DUS VWV were significantly different and carotid maps showed homogeneous thickness differences and heterogeneity in specific regions of interest identified as MR flow artifacts in the common carotid artery. J. Magn. Reson. Imaging 2009;29:901–908. © 2009 Wiley‐Liss, Inc.