In the present work, we show that after induction of mitochondrial damage by oxidative stress, in the presence of calcium, matrix DNA content decreased to 42+/-6%. Mitochondrial damage was analyzed by measuring aconitase activity, a marker enzyme of mitochondrial oxidative stress. The genes were identified by amplifying them through the polymerase chain reaction (PCR), using specific primers for each mitochondrial gene (MTCO1, MTCO2, MTCO3, MTND3, MTND5, MTATP6, MTATP8, and MTCYB). The results show that after oxidative stress, the amount of MTCO1, MTND3, and MTCYB genes in the mitochondria approximately decreased by 46, 22, and 54%, respectively. This effect was inhibited in the presence of cyclosporin A. These genes were found outside the mitochondria after permeability transition was induced. Mitochondrial integrity was evaluated by observing the activity of adenylate kinase and malate dehydrogenase.