OBJECTIVE: To evaluate the three-dimensional (3D) skeletal changes in the mandibles of Class III patients treated with bone-anchored maxillary protraction using shape correspondence analysis. MATERIAL AND METHOD: Twenty-five consecutive patients with skeletal Class III who were between the ages of 9 and 13 years (mean age, 11.10 ± 1.1 years) were treated using Class III intermaxillary elastics and bilateral miniplates (two in the infrazygomatic crests of the maxilla and two in the anterior mandible). Cone-beam computed tomography (CBCT) was performed for each patient before initial loading (T1) and at 1 year out (T2). From the CBCT scans, 3D models were generated, registered on the anterior cranial base, and analyzed using 3D linear distances and vectors between corresponding point-based surfaces. RESULTS: Bone-anchored traction produced anteroposterior and vertical skeletal changes in the mandible. The novel application of Shape correspondence analysis showed vectors of mean (± standard deviation) distal displacement of the posterior ramus of 3.6 ± 1.4 mm, while the chin displaced backward by 0.5 ± 3.92 mm. The lower border of the mandible at the menton region was displaced downward by 2.6 ± 1.2 mm, and the lower border at the gonial region moved downward by 3.6 ± 1.4 mm. There was a downward and backward displacement around the gonial region with a mean closure of the gonial angle by 2.1°. The condyles were displaced distally by a mean of 2.6 ± 1.5 mm, and there were three distinct patterns for displacement: 44% backward, 40% backward and downward, and 16% backward and upward. CONCLUSION: This treatment approach induces favorable control of the mandibular growth pattern and can be used to treat patients with components of mandibular prognathism.