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Objectives To investigate the association between toll-like receptor 9 ( TLR9) single nucleotide polymorphisms (SNPs) and human papillomavirus (HPV) infection among Chinese Han women with cervical cancer. Methods TLR9 –1486 and 2848 SNPs were investigated in patients with cervical cancer and controls using polymerase chain reaction (PCR)-restriction fragment length polymorphism. HPV16 E6 and E7 infections were assessed using PCR. Results Of 120 patients with cervical cancer and 100 controls, there was a significant association between TLR9 2848 SNP and cervical cancer risk, but there was no such association with TLR9 –1486 SNP. Frequency of the TLR9 2848 GA genotype was significantly higher in patients with cervical cancer than in controls. There was no statistically significant between-group difference in presence of HPV16 infection. Presence of HPV infection with TLR9 2848 (rs352140) GA/AA genotype increased the risk of cervical cancer 13.8-fold compared with the GG genotype. Conclusions The TLR9 2848 G/A polymorphism in Chinese Han women was associated with increased risk of cervical cancer in the presence of HPV16 infection. Further studies are necessary to uncover the functional aspect of this TLR9 2848 polymorphism.