To assess if mitochondrial DNA (mtDNA) variants are associated with mutations in BRCA susceptibility genes and to investigate the possible role of mitochondrial alterations as susceptibility markers in familial breast cancer (BC), 22 patients with or without BRCA1/BRCA2 mutations, 14 sporadic BC patients and 20 healthy subjects were analyzed. In the D-loop and in the MTND4 region, variants significantly associated with BRCA1 carriers were identified. Moreover, examination of mitochondrial haplogroups revealed X as the most significantly frequent haplogroup in BRCA1 carriers (P=0.005), and H as significantly linked to BRCA2 carriers (P=0.05). Our data suggest the involvement of the mitochondrial genome in the pathogenetic and molecular mechanism of familial BC disease.