Three Japanese patients from 2 families had a phenotype indistinguishable from that of Fukuyama-type congenital muscular dystrophy (FCMD). A full mutational analysis of the fukutin gene, however, revealed neither a 3 kb insertion (the Japanese founder mutation) nor a point mutation. A RT-PCR analysis of one of the patients revealed a normal expression of the fukutin transcript, suggesting that they have a new variant of CMD. An immunohistochemical analysis of the muscle of one case showed that the immunoreaction to alpha-dystroglycan (DG) was barely detectable on the surface membranes of muscle fibers. Immunoreactions to beta-DG, dystrophin, laminin alpha-2 chain and sarcoglycan were normal. These findings raise the possibility that the abnormality of alpha-DG is integral to the pathology seen in this variant of CMD. Analysis of POMGnT1 gene, which is causative of muscle-eye-brain disease, revealed no mutation in this case.