This study aimed to compare the pharyngeal airway volume in class I,II and III skeletal malocclusion patients using cone beam computed tomography (CBCT). This retrospective, cross sectional study was conducted on lateral cephalograms of 71 patients derived from their CBCT scans. Using the ANB angle, the patients were divided into class I,II and III malocclusion. Two observers used Dolphin 3D software to calculate the pharyngeal airway volume, airway area, minimum axial area, minimum area location, airway length and morphology. Data were analyzed using one-way ANOVA, Kruskal-Wallis test, Tukey?s test, Spearman?s correlation coefficient and multiple regression analysis. The three skeletal classes were significantly different in airway volume, minimum axial area, mean airway area and airway morphology (P<0.05). Significant differences were found in airway volume and mean airway area between class II and III patients (P<0.05). The minimum axial area and airway morphology in class III patients were greater than those in class I and II patients (P<0.05). Every one unit increase in the ANB angle decreased the airway volume by 0.261 units. The effect of ANB angle on airway volume was statistically significant and it was shown that one unit increase in the angle decreased the airway volume by 453.509 units. A significant correlation exists between the skeletal facial pattern and upper airway dimensions. In our study, the total airway volume and the mean airway area of class III patients were larger than those in class II patients.