We also found two haplotypes were associated with increased risk of BC: haplotype “AGTCA” constructed by rs3740938, rs2012390, rs1940475, rs11225394, and rs11225395 in MMP8, and haplotype “CCG” constructed by rs3918249, rs3918254 and rs3787268 in MMP9. Our results suggest that the polymorphisms of MMP8 and MMP9 may play an important role in the risk of BC in the Chinese Han population. Here, MMP9 is linked to breast cancer.