We evaluated 3-dimensional changes in the temporomandibular joints of children with skeletal Class III malocclusion and maxillary deficiency after facemask therapy for maxillary protraction. Eighteen children with anterior crossbite and a Class III molar relationship underwent facemask therapy for maxillary protraction, after which they exhibited positive overjet and a Class II molar relationship. Three-dimensional cone-beam computed tomography images of the patients were obtained before (T1) and after (T2) facemask protraction, and the 3-dimensional coordinates of the anatomical landmarks in T1 and T2 images were compared. After facemask therapy, the mandibular condyles of the patients were displaced outside, upward, and backward. Additionally, the anterior and posterior walls of the glenoid fossa had negative values for anteroposterior change. Three-dimensional analysis of the temporomandibular joint showed that facemask therapy resulted in bone apposition (to the anterior wall) and bone resorption (of the posterior wall) in the glenoid fossa. This bone remodeling resulted in upward and backward displacement of the condyle.(J Oral Sci 58, 501-508, 2016).