Objective：To study the damages within the coding region of the mitochondrial DNA in a human liver cancer cell line SMMC-7721 after exposure to different doses of X-ray irradiation.Methods: SMMC-7721 cells were radiated by different doses of X-ray (0,20,30,and 50 Gy).Primers for multiple PCR detection were designed according to the sequences of the coding region of human mitochondrial DNA,and the degree and location of mitochondrial DNA breaks were examined by LM-PCR (ligation mediated-PCR) and gene scanning technique.Results: The results of gene scanning showed the existence of X-ray sensitive breakpoints in the mitochondrial DNA coding region in human liver cancer cell line SMMC-7721,the degree of damage increased with the irradiation doses; the sensitive breakpoints were not distributed at random.The damage of heavy strand was severe than that in the light strand.Conclusion: X-ray irradiation can cause obvious damage to the coding region of the mitochondrial DNA in human liver cancer cell line SMMC-7721,and the changes of mitochondrial DNA may play a role in the clinical therapy of cancer.