In order to analyze the characteristics of dental compensation in facial asymmetry cases, three-dimensional morphological analysis was used to examine the relationships between relative position and attitude of the mandible to the cranio-maxillofacial complex and the upper and lower dentitions to their own bones. Virtualized patient models, which had been reconstructed from 16 patients with facial asymmetry, were used in this study. These models were segmented into four components, including the cranio-maxillofacial complex (CMC), the mandible (Md), the upper dentition (UD) and the lower dentition (LD), and the reference coordinates of four components were established, respectively. The geometric features of the virtualized patient models were extracted from the following three data concerning their relative positions and attitudes: Md to CMC, which represented degree of skeletal asymmetry, UD to CMC, and LD to Md, which represented dental compensation. Correlations of degree of skeletal asymmetry with relative positions and attitudes of upper and lower dentitions to the supporting bones were examined. Morphological analysis showed strong negative correlations between attitude of Md to CMC and attitude of LD to Md on the axial plane (r = -0.76), attitude of Md to CMC and attitude of LD to Md (r = -0.64), and transverse position of Md to CMC and LD to Md on the axial plane (r = -0.59). Strong positive correlations were observed between attitude of Md to CMC and UD to CMC (r = 0.92), and transverse positions of Md to CMC and UD to CMC (r = 0.80). These results indicate that the upper and lower dentitions have three-dimensionally complicated compensatory phenomena of their attitudes and positions for intermaxillary jaw discrepancies, i.e., dental compensation, in facial asymmetry cases. Also, it is suggested that three-dimensional elimination of dental compensation is necessary to properly improve facial asymmetry by orthognathic surgery.