The purpose of this study was to establish a new method for orthodontic diagnosis that integrates the three-dimensional (3-D) shape of a dental cast and the craniofacial morphology using a newly defined palatal reference plane. We also measured the accuracy of this new palatal reference plane as a reference for measurement and its spatial relationship to the framework of the craniofacial skeleton using lateral and frontal cephalometric radiography and maxillary dental casts, which were transferred using an anatomical face-bow. Eighteen female subjects were included in this study. The new reference plane in dental cast analysis corresponded to the A-PNS plane in the lateral view and to the J-J' plane in the frontal view, which have been shown to be sufficiently accurate as a reference for measurement. These results indicate that the application of this palatal reference plane, as a reference structure, should provide accurate and abundant 3-D data concerning malocclusion.