The role of mitochondrial DNA (mtDNA) mutations in the pathogenesis of Leber's hereditary optic neuropathy (LHON) has yet to be characterized. Several clinical features of the disease imply that nuclear genes might also be involved in its expression. We have confirmed the presence of a severe NADH:coenzyme Q1 reductase (complex I) defect in association with the A3460G mtDNA LHON mutation in cultured fibroblasts compared with age-matched controls. This defect was not seen in clonal fibroblasts with 0% mutant mtDNA developed from a heteroplasmic A3460G LHON subject, confirming the association between the A3460G mutation and the complex I defect. Cybrids prepared from the fusion of enucleated fibroblasts homoplasmic for the A3460G mutation with 206 (osteosarcoma) cells lacking mtDNA (p0) also had a severe deficiency of complex I activity. However, in A3460G LHON fusion cybrids containing a different nuclear background, A549 p0 (lung derived), this biochemical defect was not apparent in all the clones studied. These results suggest that the nuclear environment can influence the expression of the biochemical defect in LHON patients with the A3460G mutation.