Little is known about the neuropathology of Cornelia de Lange syndrome. We report a unique type of cerebral malformation combined with Cornelia de Lange syndrome in a 5-year-old female child. At autopsy, the optic systems, hypothalamic nuclei, corpus callosum and cerebellar vermis were hypoplastic, and the septum pellucidum, fornix and anterior commissure were rudimentary. The brain had malformative features of septo-optic dysplasia combined with commissural dysplasia and cerebellar vermian hypoplasia. This case suggests an interrelationship between Cornelia de Lange syndrome and midline development of the brain.