Aims: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.Methodology:Twenty-four CBCT images were obtained for young patients with type II, division 1 malocclusion. The i-CAT Vision (Imaging Sciences International, Hatfield, PA, USA) was used to view the images. Linear and angular measurements were obtained in the mid-sagittal plane. Univariate and bivariate analyses, as well as a multivariate analysis of principal components, were conducted.Results:The only metric with a statistically significant difference regarding gender was S–N major in the male participants. The metrics SNA–SNB and SNPg are positively related and inversely proportional to the angles BA–S–N and PO–P McGregor. The inclination of the upper incisor showed an inverse relationship with the angles SNA–SNB and SNpg. The craniovertebral angle was diminished in the entire sample, and the variable that vertically relates the hyoid was independent of the other variables.Conclusions:After evaluating 24 images of young patients with type II, division 1 malocclusion using helical spiral CBCT, it was concluded that relationships exist between the cranial base structures, the structures that determine the sagittal position of the maxilla, mandible and chin, and the cervical vertebrae complex and hyoid bone.