Mitochondria have been implicated in cell transformation since Otto Warburg considered 'respiration damage' to be a pivotal feature of cancer cells. Numerous somatic mitochondrial DNA (mtDNA) mutations have been found in various types of neoplasms, including breast cancer. Establishing the mtDNA mutation pattern in breast cancer cells may enhance the specificity of cancer diagnostics, detection and prediction of cancer growth rate and/or patients' outcomes; and therefore be used as a new molecular cancer bio-marker. The aim of this review is to summarize data on mtDNA mutation involvement in breast cancer and estimate effects of resulting amino acid changes on mitochondrial protein function. In this article published mtDNA mutation analyses are critically evaluated and interpreted in the functional context.