The aim of this study was to investigate the cervical column morphology in subjects with different anteroposterior and vertical jaw relationship. The images with cone beam computed tomography of 30 female subjects aged from 19 to 41 years, comprised two groups according to the ANB angle, ie, group 1, skeletal Class II (ANB angle >5.0); and group 2, skeletal Class III (ANB angle <1.0). Moreover, The CBCT images from 18 open-bite female patients, aged 20–39 years, were compared with 28 controls, aged 23–40 years. 9 linear measurements and one angular measurement were used to assess the morphology of cervical vertebrae. Statistical analysis was undertaken using analysis of Mann-Whitney's U-test. Vertical dimension of the posterior arch of the atlas (Dorsal arch) was significantly shorter in Class II subjects (P < 0.05). Otherwise, the mean outer margin of the first cervical vertebra was significantly larger in the open bite group than in controls (P < 0.05). This study could investigate cervical vertebra morphology with come beam computed tomography in precisely as a 3-dimensional computed tomography evaluation. Cervical vertebra morphology is associated with anteroposterior and vertical skeletal pattern, although the biological significance of outer margin changes to vertical craniofacial dimensions remains unclear.