IntroductionThere is currently no consensus in the literature whether the aetiology of a Class II subdivision is dental, skeletal or both. The aim of this study was to identify and quantify skeletal and dental asymmetries in Class II subdivision malocclusions.MethodsCBCTs from 33 Class II subdivision malocclusion patients were used to construct 3D volumetric label maps. Eighteen landmarks were identified. The original scan and associated 3D volumetric label map were mirrored. Registration of the original and mirrored images relative to the anterior cranial base, maxilla and mandible were performed. Surface models were generated, and 3D differences were quantified. Statistical analysis was performed.ResultsAnterior cranial base registration showed significant differences for fossa vertical difference, fossa roll, mandibular yaw, mandibular lateral displacement and lower midline displacement. Regional registrations showed significant differences for antero‐posterior (A‐P) mandibular length, maxillary roll, A‐P maxillary first molar position, maxillary first molar yaw and maxillary first molar roll. Class II subdivision patients also show an asymmetric mandibular length as well as an asymmetric gonial angle. Moderate correlations were found between the A‐P molar relationship and fossa A‐P difference, mandibular first molar A‐P difference, maxillary first molar A‐P difference and maxillary first molar yaw.ConclusionsThis study suggests that Class II subdivisions can result from both significant skeletal and dental factors. Skeletal factors include a shorter mandible as well as posterior and higher displacement of the fossa on the Class II side, resulting in mandibular yaw. Dental factors include maxillary and mandibular first molar antero‐posterior asymmetry.