A high prevalence of cervical vertebrae anomalies (CVA) has been recently associated with various malocclusions. Our aim was to study the prevalence of CVA on lateral cephalograms in Class II subjects and to compare the findings with those obtained from cone beam computed tomography (CBCT). Standardized cephalograms of 238 Class II patients were analysed for CVA. Cephalogram and CBCT were available for an additional 21 subjects. Cephalometric values were correlated with vertebrae morphology; logistic regressions and intraobserver agreement were evaluated. Inspection of lateral cephalograms could exclude CVA in 90.3 per cent of the subjects, while 9.7 per cent showed potential fusions. No correlations were found between the cephalometric values and potential vertebrae anomalies. In the 21 patients with a CBCT and a lateral cephalogram, the visual assessment of the cephalogram yielded a potential fusion in nine cases. None could be confirmed by CBCT. A low number of potentially fused cervical vertebrae could be detected on lateral cephalograms. The possible fusions did not correlate to any cephalometric values nor could they be confirmed by CBCT, the gold standard for assessing CVA. Visual examination of a cephalogram may result in a false-positive finding and does not allow reliable diagnosis of CVA.