Background: Polycystic ovary syndrome (PCOS) is the leading cause of anovulatory infertility. Clomiphene citrate, insulin-sensitizing drugs, aromatase inhibitors, gonadotropins, or laparoscopic ovarian drilling are various methods used for ovulation induction in women with PCOS. PCOS women with high levels of anti-mullerian hormone (AMH) and free androgen index (FAI) do not respond well to ovulation induction. This prospective observational study explores the relationship between FAI and AMH levels on ovarian response to clomiphene citrate in infertile women with PCOS. Methods: This prospective observational study included 40 infertile with PCOS who underwent ovulation induction with clomiphene citrate with dose ranging from 50 to 150 mg. Participants were classified into four phenotypes by NIH consensus panel criteria. The clinical and endocrine parameters of participants who were sensitive to clomiphene were compared to those who were resistant. Results: The most common phenotype was A. There was no significant difference in clinical and endocrine parameters among phenotypes except AMH and FAI values. Women with FAI > 7.5 and AMH >7 ng/ml might be resistant to clomiphene. Conclusion: FAI and AMH values were significantly higher in women resistant to clomiphene induction. AMH and FAI may help tailor ovulation induction protocol.