Because the pharynx and the dentofacial structures have close relationship, a mutual interaction can be expected to occur between them. The literature presents skeletal malocclusion as etiology for airway morphology changes and/or vice versa. The present three-dimensional cephalometric study from computed tomography scans was carried out to investigate upper airway space in normal nasal breathing patients presenting skeletal pattern of classes II and III. In addition, the statistical analysis was done according to gender criterion. The results revealed that the majority of the airway measurements have not been affected by type of malocclusion. The three-dimensional technology used in this study also allowed the volume and surface area calculations, and no statistical significance was found. The retroglossal width and posterior nasal cavity height mean were larger in males than females in the class II group, but volume and cross-section area were not statistically significant. However, in class III group, although the differences in linear and angular measures means were not significant, the retropalatal volume and retroglossal volume and cross-section area were larger in males. The authors highlight that the evaluation of upper airway space should be an integral part of diagnosis and treatment planning to achieve functional balance and stability of the results.