Objective: Biplanar imaging systems allow for simultaneous acquisition of lateral and frontal cephalograms. The purpose of this study was to compare measurements recorded on three-dimensional (3D) cephalograms constructed from two-dimensional conventional radiographs and biplanar radiographs generated using a new biplanar imaging system with those recorded on conebeam computed tomography (CBCT)-generated cephalograms in order to evaluate the accuracy of the 3D cephalograms generated using the biplanar imaging system. Methods: Three sets of lateral and frontal radiographs of 15 human dry skulls with prominent facial asymmetry were obtained using conventional radiography, the biplanar imaging system, and CBCT. To minimize errors in the construction of 3D cephalograms, fiducial markers were attached to anatomical landmarks prior to the acquisition of radiographs. Using the 3D CephTM program, 3D cephalograms were constructed from the images obtained using the biplanar imaging system (3D cephbiplanar), conventional radiography (3D cephconv), and CBCT (3D cephcbct). A total of 34 measurements were obtained compared among the three image sets using paired t-tests and Bland–Altman plotting. Results: There were no statistically significant differences between the 3D cephbiplanar and 3D cephcbct measurements. In addition, with the exception of one measurement, there were no significant differences between the 3D cephcbct and 3D cephconv measurements. However, the values obtained from 3D cephconv showed larger deviations than those obtained from 3D cephbiplanar. Conclusions: The results of this study suggest that the new biplanar imaging system enables the construction of accurate 3D cephalograms and could be a useful alternative to conventional radiography.