Mitochondrial DNA mutations have been identified in serveral types of cancer. In breast cancer, germline and somatic mitochondrial DNA (mtDNA) mutations have been identified. A number of mtDNA mutations in breast cancer have been identified in protein-coding regions (in protein-coding genes, such as ND2, COX3, ND4, ND5 and CytB). Mutations in these structure proteins cause impaired electron transport function and lead to electron leakage and increased reactive oxygen species (ROS) production, which in turn increases oxidative stress and oxidative damage to the mitochondria, as well as to cells. These data establish an association between mtDNA mutations and breast cancer; however, there is no reliable prediction of breast cancer predisposition or progression based on mtDNA mutation patterns thus far. In this study, we used high-throughput sequencing to detect mtDNA mutations in the blood of breast cancer patients. Some of these mutations may be used as potential markers for breast cancer diagnosis.