Abstract: Objective To quantitative analyze heavy-ion induced mitochondrial DNA mutations at different doses of irradiation. Methods Clonogenic survival of human breast cancer cells MCF- 7 was measured after X-rays or carbon ions radiation. Mitochondrial DNA 4977 deletions were detected by real-time PCR and D310 point mutations were detected by cloning sequencing, respectively. Results Clonogenic survival results and D310 polymorphism distribution after radiation showed that carbon ions radiation inhibited MCF-7 cells proliferation more effectively and caused more D310 mutations than X-ray radiation, moreover, these mutants were stably accumulated in MCF-7 clones after radiation, while mtDNA 4977bp deletions induced by carbon ions radiation only temporally exist in irradiated MCF-7 cells. Conclusion A clonal-selection mechanism exists in cells after radiation. Certain mutants that affect the normal functions of mitochondria seriously could temporally existed in irradiated MCF-7 cells, then will be eliminated soon, such as 4977 deletions; whereas D310 mutants are inherited, which is indicative of its irrelevance to the mitochondrial function.