Abstract Objective: To compare the effects of clomiphene citrate and anastrozole on follicular diameter and endometrial thickness in women with polycystic ovary syndrome (PCOS). Methods: This prospective study was conducted at the private-practice setting. The study group consisted of 14 patients who received clomiphene citrate 50 mg and 14 patients received anastrozole 1 mg on day 3 of menstruation for 5 days. Follicular diameter and endometrial thickness were measured with transvaginal ultrasound on day 12 of menstruation. Results: The mean diameter of follicles in the clomiphene citrate group was not significantly differ compared with anastrozole group (13.35±4.72 mm vs 10.92±4.29 mm; p>.05, respectively). A similar effect also observed in endometrial thickness for both study groups (8.51±1.88 mm in anastrozole vs 7.49±2.09 mm in clomiphene citrate; p>.05). Conclusion: Clomiphene citrate and anastrozole were not significantly improved follicular diameter dan endometrial thickness in polycystic ovary syndrome.