Mitochondrial DNA deletions (delta-mtDNAs), originally found at high levels in patients with sporadic mitochondrial encephalomyopathies, have also been found to accumulate at extremely low levels during normal human aging, especially in long-lived postmitotic tissues such as muscle and brain. We have now quantitated the amount of one such delta-mtDNA species, the so-called 'common deletion', in brain regions from patients with Huntington's disease (HD). Surprisingly, we found a marked decrease in the amount of this delta-mtDNA in the occipital cortex and putamen as compared to age-matched controls; however, no change was found in caudate. Using immunohistochemistry of brain sections, we found no differences in the staining pattern for selected respiratory chain polypeptides between the HD and control tissues. The reduction in the amount of delta-mtDNAs in HD may be related in part to the astrocytic gliosis in the affected areas, in which the deletion-rich neurons are replaced by relatively deletion-poor astrocytes.