The role of mitochondria in the development of diseases and in processes of aging has been investigated for last few decades. These organelles have their own genome which has a number of genes coding tRNAs and proteins important in oxygen respiration. Mutagenesis of the mitochondrial genome plays a crucial role in altering mitochondria functions, which can lead to serious diseases. Moreover, the accumulation of damage to mitochondrial DNA seems to be related to aging. Ionizing and UV radiations as well as a broad array of chemical compounds may affect the extend of mitochondrial DNA damage. The activity of respiratory electron chain results in the production of reactive oxygen species, which can damage mitochondrial DNA. The extent of mitochondrial DNA damage depend on the activity of DNA repair pathways. Research on genetic basis of mitochondrial diseases employ transmitochondrial mice, containing laboratory-induced specific mutations, allowing determination the relationship between changes in mitochondrial genome and disease phenotype.