Marinesco-Sjögren syndrome (MSS) is an autosomal recessive multiorgan disorder showing clinical and genetic heterogeneity. The key features of MSS include cerebellar ataxia, early bilateral cataracts, delayed motor development, and varying degrees of mental retardation. Patients with a subtype of MSS with myoglobinuria and neuropathy have been linked to chromosome 18qter, and recently a locus for classical MSS has been localized on chromosome 5q31. To determine the importance of myopathy in this disorder apart from the CNS based disability and to establish the pattern of muscle involvement and degree of its severity. Muscle computed tomography (CT) investigations were carried out in nine Finnish MSS patients homozygous for markers around the MSS locus on chromosome 5q31. Patients with severe clinical disability showed severe and generalized muscle degeneration. Muscle CT findings in patients with relatively severe clinical picture were characterized by severe involvement of the posterior thoracic and pelvic muscles, and almost all thigh muscles. In the legs the peronei and posterior compartment muscles were severely degenerated. The group of patients with moderate severity of disease showed the same pattern of involved muscle, albeit with lower degree of muscle degeneration. Patients with MSS linked to chromosome 5q31 have a severe progressive myopathy, the extent of which may remain largely unrecognized because of the CNS involvement.