BACKGROUND Patients with long-lasting bilateral optic atrophy showed typical clinical features of autosomal dominant optic atrophy (ADOA). Molecular genetic analysis identified them as atypical cases of Leber's hereditary optic neuropathy (LHON). METHODS Three patients with bilateral optic atrophy and central scotomas of their visual fields were clinically diagnosed with ADOA. Samples of lymphocytic genomic DNA were amplified with polymerase chain reaction, and analysis of the coding exons including the flanking intron/UTR sequences of the OPA-1 gene was performed. However, no ADOA-associated mutations were found. We therefore analysed the total lymphocyte mitochondrial DNA for all common LHON mutations in these patients. RESULTS Three patients from three unrelated pedigrees (two men, one woman) who were clinically diagnosed as suffering from ADOA did not harbor any typical mutation of the OPA-1 gene. However, analysis of their mitochondrial DNA showed that they harbored the 3460, 11778, and 14484 LHON mutations. The patients were identified as atypical cases of LHON. The pedigrees of the patients fulfilled the criteria for both dominant and mitochondrial-maternal transmission in all cases. The clinical picture of LHON differed remarkably from the classic course of LHON. CONCLUSIONS To identify atypical LHON patients with bilateral optic atrophy and central scotomas in the visual field and to distinguish them from ADOA patients, careful molecular genetic analysis is necessary. In these rare cases, only double examinations of both the genomic and the mitochondrial DNA will allow these patients to be adequately advised.