BACKGROUND: The aim of this study was to evaluate the effects of metformin and acarbose on insulin resistance, hormone profiles and ovulation rates in patients with clomiphene citrate-resistant polycystic ovary syndrome (PCOS). METHODS: Thirty clomiphene citrate-resistant patients were selected randomly and divided into two groups. Group I was treated with 100mg/day clomiphene citrate and 300mg/day acarbose 100mg/day orally. for 3 months. Group II was treated with clomiphene citrate 100mg/day and metformin 1700mg/day orally, for 3 months. Serum fasting insulin and glucose, FSH, LH, estradiol.. progesterone. prolactin and total testosterone levels plus body mass index (BMI) were measured before and after treatment. Follicle growth was followed by transvaginal ultrasonography. RESULTS: LH:FSH ratio and total testosterone concentrations decreased (P < 0.05) and ovulation rates increased in both groups. Reduction in weight and BMI was only significant in the acarbose group. CONCLUSIONS: Both treatment modalities were effective in the treatment of insulin resistance and improving ovulation rates. Increase in the number of eumenorrhoeic and norm oinsulinaernic cases and decrease in the number of insulin-resistant cases were significant in both groups (P < 0.05). Ovulation rate was greater in the metformin group in the second month of therapy (P < 0.05). Acarbose was found to be a safe and effective agent that could be used in cases with clomiphene-resistant PCOS.