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Although facial asymmetry in hemifacial microsomia (HFM) is well documented in the literature, no studies have concentrated on the morphology of the cranial base. This study aimed to evaluate the endocranial morphology in patients with HFM. Consecutive patients with unilateral HFM treated at a craniofacial center from 2000 to 2012 were included. The patients were grouped according to severity on the basis of the Kaban-Pruzansky classification: mild (0–1), moderate (2a), and severe (2b–3). Skull base angulation and transverse craniometric measures were recorded and then compared with those of age-matched controls.A total of 30 patients (14 males, 16 females) averaging 7.5 years of age (range, 1.1–15.7 y) were included. Four patients were classified as mild; 12, as moderate; and 14, as severe. The mean cranial base angle was found to be between 179 and 181 degrees with no significant difference between the severity groups (P = 0.57). The mean cranial base angle did not differ significantly in the patients compared with the controls(179.6 vs 180.0; P = 0.51) No significant differences between the affected and unaffected sides in the patients were found in distances from the midline to hypoglossal canal, internal acoustic meatus, lateral carotid canal, medial carotid canal, foramen ovale, and rotundum. There were no significant differences in transverse measurements between the severity classes using the same landmarks (P = 0.46, P = 0.30, P = 0.40, P = 0.25, P = 0.57, and P = 0.76, respectively). The cranial base axis is not deviated in the patients with HFM compared with the age-matched controls, and there exists little difference in endocranial morphologic measurements with increasing severity of HFM. These data are interesting, given the role of the cranial base in facial growth and the varying hypotheses regarding the mechanism of disease in HFM.