Nucleic acids circulating in blood plasma and other biological fluids are of interest as potential markers for the diagnosis of various pathologies and the monitoring of stresses. Mitochondrial DNA (mtDNA) is a more vulnerable target for many genotoxic agents than nuclear DNA, and mutations in the mitochondrial genome can serve as markers for many diseases. In the present study, extracellular mtDNA with mutations was assayed in the blood plasma of mice exposed to X radiation at a dose of 5 Gy. For this purpose, heteroduplexes obtained by the hybridization of mtDNA PCR amplicons (ND3 gene and D loop region) from the blood plasma of irradiated and control mice were cleaved with CEL endonuclease, a mismatch-specific enzyme. The total amount of mtDNA (ND4 gene) copies vs. nuclear DNA (GAPDH gene) was measured by real-time PCR. The content of mtDNA with mutations in murine blood plasma remained high within one month after irradiation but varied with time. The measurements were performed on days 1, 4, 8, 14, and 28 after irradiation, and the maximum level was detected on day 14. The elevated content of extracellular mutant mtDNA in blood plasma of X-irradiated mice is a sensitive candidate biomarker for the assessment of radiation injury and effects of other genotoxic agents.