Schizencephaly is an uncommon congenital malformation of neuronal migration characterized by a gray matter—lined cleft extending from the pial surface to the ependymal surface of the lateral ventricles. Its etiology is heterogeneous and consists of hereditary factors or destructive processes that occur during the second trimester of pregnancy. We report 2 cases with schizencephaly and thrombophilia caused by mutations of the methyltetrahydrofolate reductase and the factor V Leiden genes. Their clinical presentations included motor deficits and mild cognitive deficits.