Leber's hereditary optic neuropathy (LHON) is a maternally inherited disorder leading to rapid, painless, bilateral and usually permanent central vision loss in young adults, males are preferentially affected. The maternal transmission of this visual dysfunction in LHON families suggested that mutations in the mitochondrial DNA (mtDNA) are the molecular bases of the disorder. The ND1 G3460A, ND4 G11778A and ND6 T14484C mutations in the genes encoding the subunits of respiratory chain complex I, account for more than 50% of LHON families worldwide. These three mutations are designated to be primary mutations because they impart a high risk for LHON expression. However, matrilineal relatives within and among families, despite carrying the same LHON-associated mtDNA mutation(s), exhibit a wide range of onset, severity, and the progression of visual impairment. These findings strongly indicated that the LHON-associated primary mutation(s) are the primary factors underlying the development of vision loss, but they themselves are insufficient to produce a clinic phenotype. The prone to male, incomplete penetrance, and phenotypic variability of vision loss suggest that other modifier factors including personal factors, environmental factors, nuclear modifier genes and mitochondrial haplotypes contribute to the phenotypic expression of these mtDNA mutations. In particular, the mitochondrial haplotypes may play a synergic role in the development of vision loss in the families carrying the LHON-associated primary mtDNA mutation(s).