Purpose To investigate the distribution of polymorphisms of quinone oxidoreductase 1 (NQO1) C609T gene in breast cancer patients, and to analyze the relationship with breast cancer molecular subtype. Methods Genotyping of C609T rs1800566 lo-cus of NQO1 gene in peripheral blood of 248 cases of female breast cancer were detected using high-throughput TaqMan MGB real-time fluorescence quantitative PCR technology, while the detection of ER, PR, HER-2 and Ki-67 in cancerous tissues were used with immu-nohistochemical staining and FISH gene amplification. Results Among 248 cases of breast cancer patients, CC genotype accounted for 27. 42% (68/248), CT genotype accounted for 49. 60% (123/248), TT genotype accounted for 22. 98% (57/248), which con-sistent with Hardy-Weinberg equilibrium law genetic (P>0. 05). 5 cases of HER-2 (++) who did not undergo FISH testing were re-moved, all the rest were done with FISH detection. Luminal A type accounted for 15. 2% (37/243), Luminal B type accounted for 51. 4% (125/243), HER-2 overexpression type accounted for 19. 8% (48/243), basal cell type accounted for 13. 6% (33/243). Compared with patients carrying the CC genotype, ER and PR positive rates in breast cancer patients carrying CT and TT genotype was significantly higher (P<0. 05), while there was no statistically difference on the expression of HER-2 and Ki-67 proteins in two groups (P>0. 05). There was no statistically difference on distribution of C609T polymorphism of NQO1 gene among different molecular sub-types of breast cancer (P>0. 05). Conclusions Here is no relationship between C609T polymorphism of NQO1 gene and breast cancer molecular subtype, miss rate of NQO1 ( CT+TT) in basal cell carcinoma is lower, and its gene polymorphism may provide the reasonable explanation to the heterogeneity of breast cancer molecular subtype.