Over early fetal life cerebral and craniofacial morphogenesis proceed in embryological intimacy. Therefore, craniofacial shape differences between schizophrenia patients and controls are informative of developmental disturbance(s) in cerebral-craniofacial morphogenesis. 3D craniofacial coordinates were calculated from interlandmark distances for 169 patients with DSM-III-R schizophrenia and 78 matched normal controls. These were analysed using geometric morphometrics with visualisation of the resultant statistical models. Patients of both sexes were characterised by an intricate topography of 3D shape change involving lengthened lower mid-facial height, shortened upper mid-facial height, nasion located posteriorly and a wider face posteriorly; there was sex-specific rotation of the midface such that the base of the nose is more anterior in female patients but more posterior in male patients. Importantly, there were sex-specific asymmetries: in males, controls evidenced marked directional asymmetry while patients showed reduced directional asymmetry; conversely, in females controls evidenced little directional asymmetry while patients showed marked directional asymmetry. In schizophrenia, the topography of craniofacial dysmorphology appears to reflect subtle disruption to a critical 3D trajectory of embryonic-fetal craniofacial growth, particularly along the midline, with disturbance to the establishment of normal asymmetries in a sex-related manner.