Cephalometry is a standard diagnostic tool in orthodontic and orthognathic surgery fields. However, built-in magnification from the cephalometric machine produces double images from left-and right-side craniofacial structures on the film, which poses difficulty for accurate cephalometric tracing and measurements. The cone-beam computed tomography (CBCT) images not only allow three-dimensional (3D) analysis, but also enable the extraction of two-dimensional (2D) images without magnification. To evaluate the most reliable cephalometric analysis method, we extracted 2D lateral cephalometric images with and without magnification from twenty full-cranium CBCT datasets; images were extracted with magnification to mimic traditional lateral cephalograms. Cephalometric tracings were performed on the two types of extracted 2D lateral cephalograms and on the reconstructed 3D full cranium images by two examiners. The intra-and inter-examiner intraclass correlation coefficients (ICC) were compared between linear and angular parameters, as well as between CBCT datasets of adults and children. Our results showed that overall, tracing on 2D cephalometric images without magnification increased intra-and inter-examiner reliability, while 3D tracing reduced inter-examiner reliability. Angular parameters and children’s images had the lowest inter-and intra-examiner ICCs compared with adult samples and linear parameters. In summary, using lateral cephalograms extracted from CBCT without magnification for tracing/analysis increased reliability. Special attention is needed when analyzing young patients’ images and measuring angular parameters. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.