Spatial registration and fusion of ultrasound (US) images with other modalities may aid clinical interpretation. We implemented and evaluated on patient data an automated retrospective registration of magnetic resonance angiography (MRA) carotid bifurcation images with 3-D power Doppler ultrasound (PD US) and indirectly with 3-D B-mode US. Volumes were initially thresholded to reduce the uncorrelated noise signals. The registration algorithm subsequently maximized the mutual information measure between the PD US and 3-D MRA via iterative simplex search to find best "rigid body" transformation. We rated the performance of the algorithm visually on (n = 5) clinical MRA and 3-D PD US datasets. We also evaluated quantitatively the effect of thresholding, initial misalignment of the paired volumes and the reproducibility registration. We investigated the effect of image artefacts by simulation experiments. Preregistration misalignments of up to 5 mm in the transaxial plane, up to 10 mm along the axis of the carotids and up to 40 degrees resulted in 107 of 110 successful registrations, with translational and rotational errors of 0.32 mm +/- 0.3 mm and 1.6 +/- 2.1 degrees. The algorithm was not affected by missing arterial segments of up to 8 mm in length. The average registration time was 4 min. We conclude that the algorithm could be applied to 3-D US PD and MRA data for automated multimodality registration of carotid vessels without the use of fiducials.