Machado-Joseph disease (MJD) is an autosomal dominant neurodegenerative disorder caused by expansion of a polyglutamine tract in the disease protein. In this study of brains from four autopsied MJD patients, we have demonstrated immunohistochemically that expanded polyglutamine stretches largely accumulate as inclusions in neuronal nuclei, and less frequently are distributed in the nucleoplasm in a diffuse pattern. These nuclear abnormalities involved many neurons covering a wide range of central and peripheral nervous system regions, including the cerebral cortex, thalamus and autonomic ganglia that have been categorized previously as spared regions by conventional pathological studies. These lesions, newly recognized by polyglutamine immunohistochemistry, may be responsible for the cerebral cortical dysfunctions or autonomic abnormalities pointed out in MJD patients by the recent clinical and neuroradiological studies.