Recent studies indicate an important role of endogenous oxidative stress in the onset and/or in the progression of mitochondrial encephalomyopathies. In particular, the increased production of radical species caused by altered mitochondrial functionality could affect both mitochondrial and nuclear DNA integrity. We performed the micronucleus assay coupled with fluorescence in situ hybridization (FISH) to detect chromosome damage in peripheral blood lymphocytes in a group of patients affected by different forms of mitochondrial encephalomyopathies. Moreover the comet assay has been carried out to detect primary and oxidative damage in the nuclear DNA. Our results show a significant presence of both DNA and chromosome damage in patients compared to a matched group of controls. A reduction in DNA alterations is also observed in patients after treatment with coenzyme-Q10.