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Black Bone (BB) magnetic resonance imaging (MRI) is a nonionizing imaging method and a recent alternative to computed tomography (CT) in the examination of cranial deformities. The purpose of this study was to compare BB-MRI and routine 3D-CT in the preoperative evaluation of patients with craniosynostosis. At our center, we have routinely performed preoperative CT of the skull and brain MRI for patients with clinical suspicion of craniosynostosis. We recently changed our MRI protocol into one that includes sequences for the evaluation of both brain anatomy and skull bone and sutures by BB-MRI. A semi-automatic skull segmentation algorithm was developed to facilitate visualization. Both BB-MRI and 3D-CT were performed on 9 patients with clinical craniosynostosis, and the images were evaluated by two craniofacial surgeons, one pediatric neurosurgeon, and two neuroradiologists. We obtained informative 3D images using BB-MRI. Six (6/9) patients had scaphocephaly, 1 (1/9) patient had unicoronal synostosis, and 2 (2/9) patients had lambdoid synostosis. The affected synostotic sutures could be identified both by BB-MRI and by 3D-CT in all patients. Intra-rater and inter-rater reliability for rating the calvarial sutures was high. However, the reliability for rating the intracranial impressions was low by both imaging methods. BB-MRI is an alternative to 3D-CT in the preoperative evaluation of patients with craniosynostosis. BB-MRI provides information not only on cranial sutures and intracranial impressions but also on the brain structure in one imaging session. This method can replace ionizing radiation-based methods in analyzing skull deformities. [ABSTRACT FROM AUTHOR]