Objective: The study was conducted to determine whether there were differences in COX-2 expression in endometrial women with PCOS compared to fertile women. Methods: This study is a case-control study investigating the relationship between exposure (research factors) and disease, by comparing case group and control group based on their exposure status. The samples of this study were infertile polycystic ovary syndrome patients who were treated at the Sekar Fertility Clinic in Dr. Moewardi Hospital Surakarta, and fertile women seeking treatment at Dr. Moewardi Hospital Surakarta. The number of samples were 60 subjects consisting of 30 PCOS patients and 30 fertile women. The expression of COX-2 in endometrial biopsy LH + 5 until LH + 10 which meet the inclusion with Rotterdam criteria and exclusion criteria was checked by immunohistochemistry. The data was analyzed using the Mann-Whitney test. Results: The mean COX-2 expression in PCOS (10.83 ± 5.35) in fertile women (37.00 ± 7.76), p = 0.005. Regression test of COX-2 by adjusting external variables (occupation, age, education, menstrual disorders, familial history, menstrual cycle, menarche, obesity, contraception history) shows also higher expression in PCOS patient with OR = -7.063; CI = 0.462–108.066; p = 0.160. Conclusion: COX-2 expression in endometrium of women with PCOS is lower than it is in fertile women.