The main obstacle to high-resolution (<1.5 mm isotropic) 3D diffusion-weighted MRI is the differential motion-induced phase error from shot-to-shot. In this work, the phase error is addressed with a hybrid 3D navigator approach that corrects motion-induced phase in two ways. In the first, rigid-body motion is corrected for every shot. In the second, repeatable nonrigid-body pulsation is corrected for each portion of the cardiac cycle. These phase error corrections were implemented with a 3D diffusion-weighted steady- state free precession pulse sequence and were shown to mitigate signal dropouts caused by shot-to-shot phase inconsistencies compared to a standard gridding reconstruction in healthy volunteers. The proposed approach resulted in diffusion contrast more similar to the contrast observed in the reference echo-planer imaging scans than reconstruction of the same data without correction. Fractional anisotropy and Color fractional anisotropy maps generated with phase-corrected data were also shown to be more similar to echo-planer imaging reference scans than those generated without phase correction. Magn Reson Med 70:466–478, 2013. © 2012 Wiley Periodicals, Inc.