The aim of this study was to perform a morphometric analysis of the skull base to understand the mechanism of asymmetry between malformational and deformational plagiocephaly. Since 1988, we have carried out 102 CT scans with three-dimensional reconstruction of the endocranial side of the skull base. There were 20 cases of malformational plagiocephaly, consisting of 18 unicoronal synostoses (UCS) and two unilambdoid synostoses (ULS), and 82 cases of plagiocephaly without synostosis, made up of 60 cases of frontal plagiocephaly (FP) and 22 of occipital plagiocephaly (OP). The skull base asymmetry was analyzed in three ways: (1) the hemibases and the cranial fossa angles were compared with each other; (2) the structural asymmetry of the chondrocranium was calculated; and (3) the architectural asymmetry was measured in relation to the medio-labyrinthine plane. The skull base asymmetry of malformational plagiocephaly was located in the anterior and middle cranial fossae for UCS and in the posterior and middle cranial fossae for ULS. The asymmetry was the result of a localized structural anomaly of the chondrocranium. The asymmetry of deformational plagiocephaly corresponded to a distortion in relation to the medio-labyrinthine plane while the chondrocranium remained symmetric. The skull base asymmetry of malformational plagiocephaly is secondary to a localized malformation of the chondrocranium, and that of the deformational plagiocephaly is secondary to an architectural deformation.