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Objective: To examine the association between Single nucleotide Polymorphisms of toll-like receptors (TLR) 9 rs352139 and rs352140 and endometriosis.Methods: 104 cases with endometriosis (endometriosis group) and 100 other cases as a controlled group were investigated.DNA of both groups was studied by PCR followed by restriction digestion and sequencing to determine genotype and alleles frequencies.Analysis was carried out using SPSS 16.0 (SPSS,Inc.,Chicago,IL,USA).Chi square test and logistic binary regression test was performed in order to compare the genotype and alleles frequencies.All p-values were calculated.A p-value<0.05 was considered statistically significant.