OBJECTIVES: Few studies have described morphological deviations in obstructive sleep apnoea (OSA) patients on two-dimensional (2D) lateral cephalograms, and the reliability of 2D radiographs has been discussed. The objective is to describe the morphology of the cervical vertebral column on cone beam CT (CBCT) in adult patients with OSA and to compare 2D lateral cephalograms with three-dimensional (3D) CBCT images. METHODS: For all 57 OSA patients, the cervical vertebral column morphology was evaluated on lateral cephalograms and CBCT images and compared according to fusion anomalies and posterior arch deficiency. RESULTS: The CBCT assessment showed that 21.1% had fusion anomalies of the cervical column, i.e. fusion between two cervical vertebrae (10.5%), block fusions (8.8%) or occipitalization (1.8%). Posterior arch deficiency occurred in 14% as partial cleft of C1 and in 3.5% in combination with block fusions. The agreement between the occurrence of morphological deviations in the cervical vertebral column between lateral cephalograms and CBCT images showed good agreement (κ = 0.64). CONCLUSIONS: Prevalence and pattern in the cervical column morphology have now been confirmed on CBCT. The occurrence of morphological deviations in the cervical vertebral column showed good agreement between lateral cephalograms and CBCT images. This indicates that 2D lateral cephalograms (already available after indication in connection with, e.g. treatment planning) are sufficient for identifying morphological deviations in the cervical vertebral column. For a more accurate diagnosis and location of the deviations, CBCT is required. New 3D methods will suggest a need for new detailed characterization and division of deviations in cervical vertebral column morphology.