There is increasing evidence for a role of defects of mitochondrial DNA in the etiology of neurodegenerative disorders such as Parkinson's and Alzheimer's disease as well as in normal aging. In several studies a biochemical defect of complex I of the respiratory chain (NADH dehydrogenase, EC 184.108.40.206) has been found in the substantia nigra of Parkinsonian brains. Thus, mutations of mitochondrial genes encoding subunits of complex I could contribute to the pathogenesis of Parkinson's disease. A heteroplasmic G5460A mutation affecting the ND2 subunit of NADH dehydrogenase was detected in several brains of patients with idiopathic Parkinson's disease. Since this mutation is heteroplasmic we were interested in the distribution of mutated and wild-type mitochondrial DNA in different brain areas. Relative levels of mutated DNA were quantified in a large number of anatomical regions using DNA extracted from formalin-fixed and paraffin-embedded brain tissue. DNA was amplified by the polymerase chain reaction and digested employing the restriction enzyme Hphl. The proportion of mutated DNA was determined by laser densitometry. In addition, genotype-phenotype analyses were performed on sections of the substantia nigra with the aid of an automated image analysis system. Ratios of mutant to wild-type DNA varied between 44% and 98%. However, there was no systematic relationship between mutated DNA ratios and ontogenetically related brain areas suggesting that the observed regional heterogeneity of mitochondrial DNA heteroplasmy is most likely due to random segregation during development. Therefore, tissue-specific differences in the sensitivity to pathogenic effects of the ND2(5460) mutation or the influence of additional susceptibility genes may be envisioned.