In addition to a distinct malformation (pachymicrogyria, heterotaxic lamination of the cerebellar cortex, olivary dysplasia), unusual degenerative changes were found in the nervous system of 2 unrelated babies with the Zellweger syndrome. Cerebral clefts were present in 1 case. In both infants there was neuron loss and accumulation of glial nodules and globoid cells in the gray matter as well as degeneration of the white matter. There was fatty change in astrocytes and diffuse gliosis. Neurons in the column of Clarke and the lateral cuneate nucleus showed peculiar fibrillary changes. Cytoplasmic inclusion bodies were seen in the spinal ganglia. Swelling of cortical astrocytes was remarkable in the older infant. The combination of a rare malformation with the cell changes described here gives the syndrome a unique neuropathological profile.