Abstract: Objective To investigate the somatic mutations in control region of MITOCHONDRIAL DNA (mtDNA) in patients with breast tumor in Yunnan Province. Methods The DNA of tumor tissue and peripheral blood in 28 breast cancer patients and 13 benign breast tumor patients were extracted and mtDNA D-loop HVR1 and HVR2 fragments were amplified with designed two pairs of primers by PCR. The mutations of products were screened by sequencing and compared the mutations between tumor tissue and peripheral blood. Results 8 somatic mutations in 28 breast cancer patients were found, including 309+CC (sample BC6), 309+C (sample BC20, sample BC26), 279Y (sample BC16), 297R (sample BC16), 214R (sample BC21), 190Y (sample BC61) and 204Y (sample BC64); 2 somatic mutations in 13 benign breast tumor patients were found, including 16292Y (sample BCA10) and 309+CC (sample BCA12). Conclusion Our data suggest that somatic mutations in mtDNA D-loop HVR1 and HVR2 may play a role in the pathogenesis of breast cancer in Yunnan Province.