Abstract Objectives Skull morphology and growth patterns are essential for orthodontic treatment, impacting clinical decision making. We aimed to determine the association of different cephalometric skeletal configurations on midface parameters as measured in 3D CT datasets. Materials and methods After sample size calculation, a total of 240 fully dentulous patients between 20 and 79 years of age (mean age: 42 ± 15), who had received a CT of the skull within the scope of trauma diagnosis or intracranial bleeding, were retrospectively selected. On the basis of cephalometric analysis, using MPR reconstructions, patients were subdivided into three different vertical skull configurations (brachyfacial, mesofacial, dolichofacial) and the respective skeletal Class I, II, and III relationships. Anatomic parameters were measured using a three-dimensional post-processing console: the thickness of the maxillary and palatine bones as well as the alveolar crest, maxillary body and sutural length, width and height of the hard palate, maxillary facial wall thickness, and masseter muscle thickness and length. Results Individuals with brachyfacial configurations had a significantly increased palatal and alveolar ridge thicknesses compared to those with dolichofacial- or mesofacial configurations. Brachyfacial configurations presented a significantly increased length and thickness of the masseter muscle (4.599 cm; 1.526 cm) than mesofacial (4.431 cm; 1.466 cm) and dolichofacial configurations (4.405 cm; 1.397 cm) (p < 0.001). Individuals with a skeletal Class III had a significantly shorter palatal length (5.313 cm) than those with Class I (5.406 cm) and Class II (5.404 cm) (p < 0.01). Sutural length was also significantly shorter in Class III (p < 0.05). Conclusions Skeletal configurations have an impact on parameters of the bony skull. Also, measurable adaptations of the muscular phenotype could result. Clinical relevance The association between viscerocranial morphology and midface anatomy might be beneficial for tailoring orthodontic appliances to individual anatomy and planning cortically anchored orthodontic appliances.