Cone beam CT (CBCT) has become an increasingly important source of three dimensional (3D) volumetric data in clinical orthodontics since its introduction into dentistry in 1998. The purpose of this manuscript is to highlight the current understanding of, and evidence for, the clinical use of CBCT in orthodontics, and to review the findings to answer clinically relevant questions. Currently available information from studies using CBCT can be organized into five broad categories: 1, the assessment of CBCT technology; 2, its use in craniofacial morphometric analyses; 3, incidental and missed findings; 4, analysis of treatment outcomes; and 5, efficacy of CBCT in diagnosis and treatment planning. The findings in these topical areas are summarized, followed by current indications and protocols for the use of CBCT in specific cases. Despite the increasing popularity of CBCT in orthodontics, and its advantages over routine radiography in specific cases, the effects of information derived from these images in altering diagnosis and treatment decisions has not been demonstrated in several types of cases. It has therefore been recommended that CBCT be used in select cases in which conventional radiography cannot supply satisfactory diagnostic information; these include cleft palate patients, assessment of unerupted tooth position, supernumerary teeth, identification of root resorption and for planning orthognathic surgery. The need to image other types of cases should be made on a case-by-case basis following an assessment of benefits vs risks of scanning in these situations. © 2011 The British Institute of Radiology.