The neuropathological changes found at autopsy in a case of Kearns-Sayre syndrome are described. We have previously analyzed the respiratory chain function in isolated muscle mitochondria and also described a large deletion of muscle mitochondrial DNA (mtDNA) in this case. The neuropathological examination revealed prominent neuronal degeneration and gliosis of the basal ganglia and there were bilateral areas of softening and total loss of nerve cells in the lenticular nuclei. The pallidum and caudate nucleus disclosed accumulation of iron-containing pigment. The white matter in the cerebrum, brain stem and cerebellum showed widespread and focally accentuated spongy change due to splitting of myelin lamellae. It is suggested that deficiency of respiratory chain enzymes due to the mtDNA deletion is of pathogenetic importance in the development of the described changes.