We subclassified schizencephaly based on the association with optic nerve hypoplasia (ONH) and the absence of the septum pellucidum (ASP), and then characterized their clinical presentation and prognosis. The subjects of our study consisted of 10 cases with a mean age at the final evaluation of 10 years 3 months (range, 7 months to 25 years). The subclassification of schizencephaly consisted of the septo-optic dysplasia (SOD) group (n=3), with ONH and ASP; the optic hypoplasia (OHP) group (n=2), with ONH and without ASP, and; the classical group (n=5), without ONH. The subjects with an open-lip cleft in the SOD and the classical group showed hydrocephalus, but those in the OHP group did not. The SOD and the OHP group displayed severe psychomotor retardation regardless of the cleft morphology, but in the classical group, the subjects with an open-lip cleft or with diffuse cortical dysplasia were severely retarded. The SOD and the OHP group displayed intractable epilepsy. In contrast, all subjects in the classical group showed good control of epilepsy. The results of our investigation show that the subclassification of schizencephaly based on the association with ONH and ASP is useful. The SOD group means early fetal brain injury which results in extended cortical dysplasia while the OHP group means severe destructive brain injury which results in cerebro-cerebellar disruption.