Walker-Warburg syndrome (WWS) is an autosomal recessive disorder characterized by the combined involvement of the central nervous and skeletal muscle systems. Although the molecular basis of WWS remains unknown, defects in the muscle fibre basal lamina are characteristic of other forms of congenital muscular dystrophy (CMD). In agreement with this, some forms of CMD, due to glycosyltransferase defects, display a reduction in the immunolabelling of alpha-dystroglycan, whilst beta-dystroglycan labelling appears normal. Here we describe an almost complete absence of alpha-dystroglycan using both immunohistochemistry and immunoblotting in two patients with WWS. In addition, there was a mild reduction of laminin-alpha 2. In contrast, immunohistochemical labelling of perlecan and collagen VI was normal. Linkage analysis excluded the recently identified POMT1 locus, responsible for a proportion of WWS cases. These results confirm that WWS is a genetically heterogeneous condition and suggest that disruption of the alpha-dystroglycan/laminin-alpha 2 axis in the basal lamina may play a role in the degeneration of muscle fibres in WWS-also in cases not due to POMT1 defects.