A new revolution in three-dimensional radiologic advances in dentistry was introduced in the year 1998, as cone beam computed tomography (CBCT). Over the years, it has become an increasingly popular technique in orthodontic diagnosis, treatment planning, and research. This rise in its popularity has been facilitated by the relative advantages of three-dimensional (3D) over 2D radiography. CBCT imaging involves only a minimal increase in radiation dose relative to combined diagnostic modern digital panoramic and cephalometric imaging. A combination of volumetric reconstruction and multiplanar views can provide the orthodontic clinician with skeletal hard tissue, soft tissue, dentition, and airway information. Despite many suggested indications of CBCT, scientific evidence that its utilization improves diagnosis and treatment plans or outcomes has only recently begun to emerge. This article provides a comprehensive review of the application of CBCT in orthodontics. The current indications for CBCT in standard orthodontic diagnosis include impacted teeth, cleft lip, and palate and skeletal discrepancies requiring surgical intervention, root resorption, supernumerary teeth, temporomandibular joint (TMJ) pathology, facial asymmetry, temporary anchorage devices, root morphology and angulation; alveolar boundary conditions; maxillary transverse dimensions and maxillary expansion, and vertical malocclusion. Advanced CBCT software applications can be used to quantify airway space in the cases of obstructive sleep apnea, perform superimpositions to semiquantitatively visualize changes over the hard and soft tissues, including the TMJ and airway.