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This study aimed to establish a three-dimensional (3D) cephalometric analysis of craniofacial morphology and discuss its theoretical usefulness in orthognathic patients. Cone-beam computed tomography (CBCT) images of Japanese subjects with skeletal Class I malocclusion before treatment were selected from among 1000 patients so that samples matched a historic 2D cephalometric cohort with normal occlusion using propensity score matching. In each CBCT image, 67 3D measurements were calculated based on manually identified landmarks. The mean and standard deviation of the measurements were calculated and used as the normative range for each sex. To confirm the usefulness of the 3D measurements, pre- and post-treatment CT data of nine jaw deformity patients who underwent orthognathic surgery with two-dimensional planning (2DP) in the past were used. Pre- and post-treatment CT values were evaluated with a paired t-test as well as a Z-score, which was calculated using the aforementioned normative range, and then categorized into five groups ("deteriorated", "no improvement", "over-treatment", "no change", "improvement") with -1 < Z-score < 1 considered normal. Fifty-six patients were matched to normal skeletal 1 subjects. The normative range of 67 items indicating 3D craniofacial morphology of the Japanese was calculated. Postoperatively, the horizontal position of the pogonion to the mid-sagittal plane significantly decreased (p = 0.043) and "improved"; however, the ramus axis on the right side significantly increased (p = 0.005) and "deteriorated". Maxillary yaw and the horizontal position of the gonion also tended to "deteriorated". The normative range for the 3D cephalometric analysis in Japanese has been established. Given findings of deteriorated maxillomandibular yawing after surgery when using conventional 2DP, 3D cephalometric measurements should be used when planning jaw positions after surgery for orthognathic patients., Competing Interests: Declaration of competing interest The software programs used for this study, the 3D image processing software (Mimics Materialise), and the craniofacial surgery planning software (Materialise ProPlan CMF), were loaned by Materialise Japan (Yokohama)., (Copyright © 2022 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.)