A male infant was born with severe hydrocephalus, bilateral cleft lip/palate, left anophthalmos and right microphthalmos, and an equino-varus foot deformity. Imaging studies showed enlarged lateral ventricles, apparent absence of the corpus callosum and a midline density in the third ventricular region. He had a normal male karyotype. He was severely mentally retarded and died suddenly at 7 years of age. Neuropathological examination of the brain revealed enlarged and polygyric cerebral hemispheres, due to congenital obstructive hydrocephalus, and secondary thinning of the corpus callosum. An unusually large neuronal hamartoma filled the interpeduncular fossa and third ventricle. It was continuous posteriorly with the left thalamus and so was classified as diencephalic rather than as hypothalamic. The right optic nerve merged with the hamartoma, whereas the left nerve was absent. Microscopically the hamartoma consisted of mature grey matter interspersed with narrow bands of white matter. No immature or non-neural elements were identified. This combination of diencephalic neuronal hamartoma, hydrocephalus, ocular and craniofacial abnormalities has not, to our knowledge, previously been described.