Single nucleotide polymorphisms (SNPs) are accumulated frequently in the mitochondrial displacement loop (D-loop) in various types of cancer, and their association with cancer risk and disease outcome has been extensively identified. We have identified specific risk-associated SNP for familial breast cancer patients previously. In this study, we investigated the association between age-at-onset and the SNPs in familial breast cancer patients. The SNP sites of nucleotides 16 311 T/C were identified for their association with age-at-onset using the log-rank test. The age-at-onset of the patients with the minor allele C genotype was significantly earlier than that of patients carrying the T genotype at the site 16 311 (p = 0.032). Accordingly, the genetic polymorphisms in the mitochondrial D-loop are predictive markers for age-at-onset in familial breast cancer patients, which may help to identify familial breast cancer patient subgroups at high risk of early onset.