We compared the neuropathological findings in two cases of the Walker-Warburg syndrome (WWS) with those in 6 of Fukuyama-type congenital muscular dystrophy (FCMD). Remarkable differences were noticed between the two conditions. The central nervous system (CNS) dysplasia in WWS, which involved diffuse agyria and hydrocephalus, was more severe than that in FCMD. In WWS the septum pellucidum was absent, and the corpus callosum, basal ganglia and thalami were markedly hypoplastic. The cerebellum was severely hypoplastic and the vermis was partly absent. The pyramidal tracts could not be identified. On the other hand, the general configuration of the CNS was well preserved in FCMD. The cerebral cortices exhibited diffuse or focal micropolygyria with or without a few pachygyric lesions, but the severity was variable. The cerebellum was not hypoplastic, but exhibited focal micropolygyria. The pyramidal tracts were aberrant. WWS and FCMD, however, did not show any distinct differences on microscopic analysis of the cerebral cortices. There was leptomeningeal glio-mesenchymal overgrowth, and the horizontal lamination of the nerve cells was distorted throughout by proliferating gliovascular bundles or septa. We found in this study that the CNS pathology in WWS was compatible with type II lissencephaly, and thus differed from that in FCMD. Hypoplasia of the cerebellum and a partial absence of the vermis also seemed to be predominant features of WWS, which can be used to differentiate WWS from FCMD. In this study, we concluded that FCMD and WWS are different disease entities because they differ in their clinical manifestations, including eye lesions and CNS pathology, and because no familial concomitance of FCMD and WWS has been reported.