The etiology of Angle class III malocclusion with facial asymmetry has not been fully elucidated. To investigate the etiology, patients with asymmetric prognathism (n = 30) from a single institution were assessed for previously undiagnosed torticollis and cranial base asymmetry. Presence of torticollis was determined by measuring restricted head movement when turning the head against a wall and cranial base tilt with upward gaze. Cranial base asymmetry was evaluated by preoperative three-dimensional computed tomography scans. Thirty-one percent of patients with prognathism presented with concurrent facial asymmetry. In patients with asymmetric prognathism, cranial base tilt was present on upward gaze in all patients; mean angle between head and wall was 31 degrees greater than that in control patients, and a 22% to 36% difference in the angle was present when comparing one side with the other. Based on these findings, all patients with asymmetric prognathism were found to be affected by torticollis. By computed tomography scan, 85% of these torticollis patients showed slight anteromedial displacement of the glenoid fossa ipsilateral to torticollis, and 73% demonstrated temporal fossa shift of 4 mm or greater. The current study demonstrates a strong association between asymmetric class III malocclusion, torticollis, and cranial base asymmetry. We conclude that undiagnosed torticollis is a likely etiology for otherwise idiopathic cranial base asymmetry and that cranial base asymmetry in turn causes facial asymmetry and malocclusion. This study highlights the importance of evaluating cranial base asymmetry and torticollis in patients with class III malocclusion to allow for earlier treatment and improved outcomes.