Different vertical facial patterns may present different bone and gingival thicknesses at the molar level and can be influenced by the dental compensations that manifest in the presence of transverse bone discrepancies. A retrospective analysis was made of 120 patients divided into three groups according to their vertical facial patterns (mesofacial, dolichofacial or brachyfacial). Each group in turn was divided into two subgroups according to the presence or absence of transverse discrepancies assessed by cone-beam computed tomography (CBCT). The bone and gingival measurements were made integrating a CBCT-3D digital model of the patient dentition. In the brachyfacial patients, the distance from the palatine root to the cortical bone corresponding to the right upper first molar was significantly greater (1.27 mm) than in the dolichofacial (1.06 mm) and mesofacial (1.03 mm) (p < 0.05) patients. The brachyfacial and mesofacial patients with transverse discrepancies presented a greater distance from the mesiobuccal root of the left upper first molar and from the palatine root to the cortical bone, while in the dolichofacial individuals the distances were shorter (p < 0.05); The presence of transverse bone discrepancies in brachyfacial and mesofacial patients without posterior cross-bite implies a better dentoalveolar expansion prognosis than in dolichofacial individuals.