Breast cancer is the most frequently diagnosed female cancer all over the world. Although the molecular genetics of this disease has been the focus of many projects for over 20 years, the number of prognostic markers used in clinics is still unsatisfactory. Mitochondrial DNA mutations have been reported in many breast cancer studies. To investigate the possible role of mitochondrial inherited polymorphisms in breast cancer development we analyzed the sequence of NADH-dehydrogenase genes in cancer samples and their corresponding normal tissues. We detected increased incidence of mtDNA polymorphisms, in particular very rare polymorphisms such as A4727G, G9947A, A10044G, A10283G, T11233C, and C11503T. Our report supports the notion that mtDNA polymorphisms establish a specific genetic background for breast cancer development and that mtDNA analysis may help in selection of cohorts that should undergo intensive screening and early detection programs.