In hemifacial microsomia (HFM), the major deficiency is seen in the mandible, but other craniofacial bony structures can be involved as well. This study was designed help establish baselines regarding Japanese craniofacial symmetry in the case of HFM symptoms that incorporate the deformity of not just the mandible but also of other craniofacial skeletal features. Six subjects between the age of 7 and 13 years were studied via three-dimensional computed tomography (3DCT) images and their occlusion. The subjects were classified as being of Pruzansky's Type II A, II B, or III. The Mandibular Deformity Scoring System (MDS), the Cranial Deformity Scoring System (CDS), and the Craniofacial Deformity Scoring System (CFDS) developed by Vaandrager are based on 3DCT reconstructions, which suggests that craniofacial morphological characteristics of HFM can be marked as the total score. We investigated the relationship between CFDS, 3D bone structure, and distinctive occlusion on each subject. The result indicated that the influence of dysplasia appeared mostly on the nasomaxillary component and on the corpus length and full length of the mandible. There were only minor differences in the lengths of ramus and lateral cranial base among the types by Pruzansky. The position of the temporomandibular joint was high compared with that of the control side because of nasomaxillary dysplasia. Therefore, regardless of the ramus length, the mandibular midline was shifted to the affected side. In the cranial area, in patients with Pruzansky type II B, the marlar bone, zygomatic arch maxilla part, and temporal part could have a much more severe appearance than in the patient with Pruzansky type II A. The CDS score for patients with Pruzansky type III were very different from patients in the other categories. CDS was conversely related to MDS; the Pruzansky's classification was not directly proportional to the CDS score.