The purpose of this study was to evaluate if Frankfort plane (FH) and plane passing through the lateral semicircular canals (LS) can be used as reference planes in three-dimensional analysis.Ten patients with facial asymmetry underwent a three-dimensional computed tomography. Computed tomographic images were processed by means of a commercial software and a personal computer to obtain a three-dimensional virtual craniofacial model. The average Frankfort plane and the plane passing through the LS were identified. The distance from the above-mentioned planes to the first upper molar and upper canine cusp was measured.It was not possible to detect an FH plane in any of the patients. Right FH, left FH, average FH, and LS plane were traced. The discrepancies among reference planes were significant in cases with severe asymmetry. A minimal discrepancy was noticed in patients with light asymmetry.In patients with severe asymmetry, the LS plane results in steady, reproducible, detectable, and closer to the patient's anatomy, representing a valid reference plane for three-dimensional computed tomography analysis.