Muscle-Eye-Brain disease (MEB) and Fukuyama type congenital muscular dystrophy (FCMD) are clinically similar autosomal recessive diseases, characterized by congenital muscular dystrophy and severe mental retardation, raising the possibility that they might be caused by mutations of the same gene. Recently FCMD was localized to chromosome 9q31-33 by linkage. We performed a linkage study in seven Finnish MEB families with 12 affected patients using markers D9S53, D9S58, D9S59 and HXB. The MEB phenotype was not linked to any of the markers. A multipoint linkage analysis excluded the entire region harboring FCMD. We thus conclude that MEB and FCMD are not allelic.