The objectives of the present study were to compare measurements of pharyngeal airway subregions on lateral cephalometric (LC) and cone beam computed tomographic (CBCT) images in relation to skeletal classes and discuss the advantages and disadvantages of these imaging formats for this type of assessment. The CBCT images were assessed via both multiplanar reconstruction (MPR) and 3-dimensional (3D) reconstruction. The LC and CBCT images from 107 patients were classified according to skeletal class: I, n = 35; II, n = 35; and III, n = 37. Linear measurements of the subdivisions of the upper airway were performed on the LC, MPR, and 3D images. In addition, area and volumetric measurements were performed on the MPR images. The relationships among imaging methods, skeletal class, and pharyngeal thirds were assessed by means of a 1-way analysis of variance (α = 0.05). No statistically significant differences in the linear, area, or volumetric measurements of the upper airway subregions were found among the skeletal classes (P > 0.05). For the linear measurements in the oropharynx and hypopharynx, greater values were observed for the LC images than for the MPR and 3D images (P ≤ 0.05). Based on the study findings, MPR images should be preferred for visualization of the pharyngeal airway subregions. However, LC imaging is preferable to 3D reconstruction.