This study investigated the association of craniofacial and glenoid fossa shapes and temporomandibular joint (TMJ) pathology in 39 orthodontic patients with signs and symptoms of TMJ disorders, using helical CT scans. Cephalometric measurements showed that 21 subjects with bilateral condylar bone change (BBC) had significantly smaller SNB angles, ramus heights and S-Ar/N-Ba ratios, as well as larger mandibular plane angles and lower anterior facial height than the 18 subjects with no condylar bone change (NBC). The average posterior slope of the left and right articular eminence in their central and lateral sections was significantly steeper in NBC than in BBC. Condylar bone change might, therefore, not only be related to the morphology of the mandible, but also of the glenoid fossa and cranial base. This appears to reflect adaptive changes in the condyle, articular eminence and cranial base in response to changes in loading.