Objectives: To test the null hypotheses that the positions of the glenoid fossae and mandibular condyles are identical on the Class I and Class II sides of patients with Class II subdivision malocclusion. Materials and Methods: Retrospective three-dimensional (3D) assessments of the positions of the glenoid fossae and mandibular condyles were made in patients with Class II malocclusion. Relative to a fiducial reference at the anterior cranial base, distances from the glenoid fossae and condyles were calculated in pretreatment cone beam computed tomographic scans of 82 patients: 41 with Class II and 41 with Class II subdivision malocclusions. The 3D distances from glenoid fossae to sella turcica in the X (right-left), Y (anterior-posterior), Z (inferior-superior) projections were calculated. Results: Patients with Class II malocclusion displayed a symmetric position of the glenoid fossae and condyles with no statistically significant differences between sides (P . .05), whereas patients with Class II subdivision showed asymmetry in the distance between the glenoid fossae and anterior cranial base or sella turcica (P , .05), with distally and laterally positioned glenoid fossae on the Class II side. (P , .05). Male patients had greater distances between glenoid fossae and anterior cranial fossae (P , .05). The condylar position relative to the glenoid fossae did not differ between the two malocclusion groups nor between males and females (P . .05). Conclusions: The null hypotheses were rejected. Patients with Class II subdivision malocclusion displayed asymmetrically positioned right-and left-side glenoid fossae, with a distally and laterally positioned Class II side, although the condyles were symmetrically positioned within the glenoid fossae. (Angle Orthod. 2017;87:847-854.)