PURPOSE: The aim of the present study was to investigate the disagreement of cephalometric analysis depending on the reference determination of midsagittal plane on three-dimensional computed tomography. MATERIALS AND METHODS: A total of 102 young women with class III dentofacial deformity were evaluated using three-dimensional computed tomography. The cranial and facial midsagittal planes were defined and the amounts of jaw deviation were calculated. The amounts of jaw deviation were compared with paired t-test (2-tailed) and Bland-Altman plot was drawn. RESULTS: The landmark tracing were reproducible (r> or =.978). The jaws relative to the cranial midsagittal plane were 10-17 times more significantly deviated than to the facial midsagittal plane (P<.001). Bland-Altman plot demonstrated that the differences between the amounts of jaw deviation from two midsagittal planes were not normally distributed versus the average of the amounts of jaw deviation from two midsagittal planes. CONCLUSION: The cephalometric analyses of facial asymmetry were significantly inconsistent depending on the reference determination of midsagittal plane. The reference for midsagittal plane should be carefully determined in three-dimensional cephalometric analysis of facial asymmetry of patients with class III dentofacial deformity.