A comparative analysis between early (stage I + II) and late (stage III + IV) stages revealed heterozygous genotypes of TLR9 rs187084 [p = 0.011, age-adjusted OR = 0.283 (0.107–0.749)] and rs352140 [p = 0.015, age-adjusted OR = 0.304 (0.117–0.790)] to be associated with early stage cervical cancer. This evidence concerns the gene TLR9 and cervical cancer.