We describe the clinical and neuropathological presentation of a male with an MECP2 mutation whose sister has Rett syndrome (RS). He presented with severe neonatal encephalopathy and died at the age of 13 months. Mutation analysis of the MECP2 gene demonstrated a 488-489 del mutation in his and his sister's copies of the gene. Post mortem examination revealed bilateral polymicrogyria in the perisylvian region. This malformation was visibly more severe than previously described in females with RS and another male with an MECP2 mutation. As bilateral polymicrogyria was described in congenital perisylvian syndrome, the presented patient could be regarded as having suffered from a severe form of this syndrome. We conclude that MECP2 screening should be considered in males with severe neonatal encephalopathy and in males and females with a bilateral polymicrogyria syndrome.