To allow a more objective interpretation of 3D carotid bifurcation images, we have implemented and evaluated on patient data, automated volume registration of 3D magnetic resonance angiography (MRA), 3D power Doppler (PD) ultrasound, and 3D B-mode ultrasound. Our algorithm maximizes the mutual information between the thresholded intensities of the MRA and PD images. The B-mode images, acquired simultaneously in the same orientation as PD, are registered to the MRA using the transformation obtained from the MRA-PD registration. To test the algorithm we misaligned clinical ultrasound images and simulated mismatches between the datasets due to different appearances of diseased vessels by removing 3D sections of voxels from each of the paired scans. All registrations were assessed visually using integrated 3D volume, surface, and 2D slice display. 97% of images misaligned within a range of 40 degrees and 40 pixels were correctly registered. The deviation from the mean registration parameters due to the simulated defects was 1.6 +/- 2.5 degrees, 1.5 +/- 1.6 pixels in X, Y and 0.7 +/- 0.7 pixels in Z direction. The algorithm can be used to register carotid images with misalignment range of 40 pixels in X, Y directions, 10 pixels in Z direction and 40 degree rotations, even in the case of different image appearances due to vessel stenoses.