The NAD(P)H:quinone oxidoreductase 1 (NQO1) enzyme is implicated in protection against oxidative stress and carcinogenesis. NQO1 C609T genetic polymorphism was reported to be associated with an increased risk for cancers, including breast cancer. However, there is still lack of evidence whether higher oxidative stress occurs in breast tissues of patients with NQO1 609 C/T and/or T/T genotypes. Mitochondrial DNA (MtDNA) 4,977-bp deletion, the most common mutation of mtDNA, was frequently detected in post-mitotic tissues of aged subjects and associated with oxidative damage. In this study, we detected the mtDNA 4,977-bp deletion in 60 breast cancers and corresponding non-cancerous breast tissues. The incidence of the common 4,977-bp deletion in non-cancerous breast tissues (48.3%) was higher than that in breast cancer (5.0%). Moreover, 63.4% of the breast cancer patients with NQO1 C/T or T/T genotypes had the deletion in their non-cancerous breast tissues. The mtDNA deletion was more frequently detected in breast tissue of NQO1 C/T carriers (65.2%) and T/T carriers (61.1%) as compared with the NQO1 C/C carriers (15.8%, P=0.003). Similar results were observed in the <50 years old (y/o) group (P=0.06) and the > or =50 y/o group (P=0.005). Our findings suggest that mtDNA 4,977-bp deletion associated with NQO1 deficiency is involved in carcinogenesis and progression of breast cancer.