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Endometriosis is characterized by the growth of endometrial outside the uterine cavity, which is found in women with subfertility and pelvic pain problems. The development in reproductive age and the decrease after menopause or ovariectomy prove that endometriosis is an estrogen dependent disease. Effect of the estrogen hormone depends on the binding to its receptor. Estrogen receptor alpha (ERa) polymorphisms which admit by PvuII enzyme restriction has associate to some womens disease like endometriosis. This Study aimed to determine the correlation between ERa 397 T/C with the risk of endometriosis. This study is an analytical observational study with the case control design. There were 70 samples which were divided into 2 groups: 35 cases (endometriosis group) and 35 controls (non-endometriosis group). The determination of genotypes and allotypes used PCR-RFLP method and the data analysis by chi square test a<0,05.The results showed that genotype frequencies of case group are 11,4% TT, 54,3% TC and 12% CC while genotype of control group are 34,3% TT, 51,4% TC and 14,3% CC with p value 0,032. Allele frequencies of case group are 38,6% T and 61,4% C while control group are 60% T and 40% C with p value 0,011. Conclusion: there is a significant correlation between the genotype and allel polymorphism of ERa gene 397 T/C with the risk of endometriosis.