The purpose of this study was to relate the facial asymmetries with possible impairments of the skull base, particularly with regard to the three-dimensional position of the glenoid fossa. Fifty-eight subjects met the inclusion criteria (25 men and 33 women) and were included in the analysis. All patients underwent three-dimensional computed tomographies. Patients were classified into 3 asymmetry groups: vertical plane asymmetries, transversal plane asymmetries (TAs), and hybrid forms. A control group, composed of 29 subjects having obstructive sleep apnea syndrome with no asymmetries, was used to compare data from the study populations. The glenoid fossa moved forward and superiorly on the affected side if compared with the healthy side both in the vertical plane asymmetry group and in the TA groups (P < 0.001). Differences were wider in the TA group. Statistically significant differences regarding the middle and posterior cranial base angles were observed between the affected side of the TA patients and the control group. We reported an amplitude reduction of the middle cranial base angle and an increase of the posterior cranial base angle in the affected side. The glenoid fossa could represent the missing link between the development of the temporal region and the ipsilateral hemimandible.