BACKGROUND: The aim of this study was to present three-dimensional (3D) structural characteristics of the mandible in the hemifacial microsomia. The mandible has six distinct functional units, and its architecture is the sum of balanced growth of each functional unit and surrounding matrix. METHODS: In order to characterize the mandibular 3D architecture of hemifacial microsomia, we analyzed the mandibular functional units of four hemifacial microsomia patients using the 3D reconstructed computed tomography (CT) images. And we compared the functional unit size between affected and non-affected side. RESULTS: The length of condyle and angle showed significant differences between affected and non-affected sides. However, the length of mandibular body showed insignificant differences. The size differences between affected and non-affected side were observed at the condyle, angle, and body in descending order. CONCLUSIONS: This preliminary study suggests that the main etiopathogenic units are condyle and angle in the hemifacial microsomia mandible. Further investigation with the increased number of subjects will be helpful to establish treatment modality by etiopathogenic targeting of hemifacial microsomia.