With violations of the mitochondrial genome associated wide range of degenerative diseases, the development of tumor pathology, aging and the processes of cell death. We investigated the levels of mitochondrial DNA (mtDNA) with mutations and their total content in the tissues of the brain, and spleen of mice exposed to X-rays at doses of 1-5 Gy, and depending on the post-radiation time (8-28 days). These same mice were analyzed for the level of mutant copies of the extra cellular mtDNA (ec-mtDNA) and its total content in blood plasma. Mutations were determined by means of CEL-I endonuclease (mismatch-specific enzyme) cleavage of heteroduplexes, obtained by hybridization of PCR amplicons of mtDNA (D-loop region) of irradiated and control mice. The changes of total amount of mtDNA (ND4 gene) copies vs. nuclear DNA (GAPDH gene) measured by real-time PCR method. The results showed that in the tissues of the brain, and of the spleen of irradiated mice (with a maximum at 8 days after exposure) the level of mutant mtDNA copies, with a subsequent decline to a 28-day post-radiation time dramatically increased. Was shown that mutagenesis of mtDNA in the brain and spleen tissues of irradiated mice, well as mutagenesis of nuclear genes, has a linear dependence on the dose X-rays. In contrast, mutant nuclear genes, the majority of mutant mtDNA copies is eliminated from the tissues of the brain and of the spleen, while maintaining them at the same level of total content of mtDNA within 28 days after irradiation in mice. The results show that during this post-radiation time in the plasma of irradiated mice high levels of ec-mtDNA with mutations, with a maximum at the 14th day in the total circulating DNA maintained. These data suggest that the mutant copies of mtDNA eliminated from tissues cells of irradiated animals in the post-radiation period. Elevated levels of ec-mtDNA with mutations in the plasma can be considered as a potential marker for the assessment of radiation injury of organism.