Facial asymmetry is often seen in patients with skeletal mandibular prognathism and is associated with deformities in the maxillofacial and head regions. The maxillofacial deviation is three-dimensional and affects not only the lateral deviation of the mandible and midface, but also the cranium. This study conducted a three-dimensional morphological evaluation of the cranial base morphology of patients with skeletal mandibular prognathism (ANB p = 0.012). Given the identified association between the structure of the head region and facial asymmetry, further studies are needed to determine the factors implicated in the growth process.