In CAG repeat diseases, affected neurons possess many cytoplasmic granules immunopositive for expanded polyglutamine stretches. Electron microscopic immunohistochemistry showed that the granules corresponded to lysosomes of primitive type. The results suggest that, in addition to the ubiquitin/proteasome pathway, mutant proteins with expanded polyglutamine stretches are involved in the lysosomal pathway for protein degradation and that this processing mechanism may serve as a target for a new therapeutic approach to CAG repeat diseases.