Current cephalometry in dentistry relies on plain lateral films to evaluate craniofacial structure of patients. This concept is based on 2D images which are difficult to apply in complicated craniofacial structures. The purpose of this study is to develop a 3D cephalometric analysis by reconstructing the 3D-CT skull images, which provides landmark identification and Downs analysis in the 3D software. This system also has the feature of multiple view windows, auto cephalometric measurement and counting, and simplified user's interface. A pilot study, using the landmark identification and cephalometric analysis which was processed by ten observers at two different times, was conducted to evaluate the accuracy and reliability of this system. The result supports this approach to be a reliable method in cephalometric analysis and worthy to research in the future.