Objective: To explore the potential roles of mitochondrial DNA somatic mutations in benign breast disease based on the entire genome of mitochondrial DNA and elucidate the relationship between benign breast disease and breast cancer. Methods: The genomic DNA of tumor tissue and peripheral blood in 28 benign breast disease patients with an average age of 33 years (range: 30-50) were extracted respectively. According to the revised Cambridge reference sequence and phylogenetic tree reconstruction, the mutations were identified and distinction was made between somatic mutations and private mitochondrial DNA mutations by haplogroup. Results: Seven somatic mutations were detected. One mutation was located in the control region whereas the other six lied in the coding region. Further analyses revealed that, out of these 6 coding-region mutations, 4 were non-synonymous and would introduce the changes of amino acids. Conclusion: The mutations of mitochondrial DNA may play potential roles in the occurrence and development of benign breast disease. Copyright © 2012 by the Chinese Medical Association.