Cone-beam CT (CBCT) was developed for the three-dimensional (3D) imaging of the maxillofacial area and has become popular in dentistry, orthodontics, and maxillofacial surgery. The advantages of CBCT include less radiation exposure (than conventional CT), less artifacts, and submillimeter spatial resolution. CBCT has been shown to produce accurate 3D images of the craniofacial region and a 1-to-1 image-to-reality ratio, which has greatly reduced errors of frontal cephalometry and improved our ability to diagnose asymmetry. Several new analyses to diagnose asymmetries on 3D images described in recent literature were reviewed, including 3D linear and angular measurements, mirror-image analysis (superimposition of the mirror image of the anatomically correct part of the anatomy over the deformity), 3D cephalometric analysis based on constructing an individual coordinate system for each facial unit or element (local coordinate systems) to differentiate them from the world coordinate system (whole head orientation), and method of application of asymmetry indices.