Traditionally, diagnosis and treatment planning of structural and three-dimensional anomalies have been performed using two-dimensional X-rays. Cone beam computed tomography (CBCT), the technology utilized in this study, allows creation of specialized images from the craniofacial region that provide more precise and reliable results. The growth of the cranial base, position and size of the cervical system, and the hyoid bone has an influence upon the morphogenesis and the growth of the maxillofacial complex. The data obtained through this current study offer a better understanding of the origin and manifestation of malocclusions, and will, therefore, offer a better therapeutic approach. The objective of the current study is to describe the measurements of the cranial base and the cranial–cervical–mandibular system in young patients with type II, division 1 malocclusion, using CBCT.