Breast cancer is the most commonly diagnosed cancer in women. Despite recent advances in breast cancer research, a comprehensive set of genetic markers of increased breast cancer risk remain elusive. Recently mitochondrial DNA (mtDNA) mutations have been found in many types of cancer, including breast cancer. To investigate the possible role of mitochondrial genetics in breast cancer predisposition and biology we analyzed the D-loop sequence of cancer patients and assigned mitochondrial haplogroup using RFLP analysis. We detected a significantly greater incidence of mtDNA polymorphisms T239C, A263G and C16207T and a significant lower incidence of A73G, C150T, T16183C, T16189C, C16223T, T16362C in patients with breast cancer compared to database controls. The mitochondrial haplogroup distribution in patients with breast cancer differs from a group of cancer-free controls and the general Polish population in that haplogroup I is over-represented in individuals with cancer. These findings suggest that mitochondrial haplogroup I as well as other polymorphic variants defined by SNPs in the D-loop may be associated with an increased risk of developing breast cancer.