This study was conducted to evaluate the efficacy of metformin compared with ovarian drilling in the treatment of clomiphene citrate (CC) resistant women with polycystic ovary syndrome. A total of 161 infertile, CC-resistant women with PCOS aged 22-34 years (mean 25.5 +/- 4.4) were evaluated prospectively during the period between January 2000 and December 2001. Patients were allocated into two groups; group 1 includes 64 women who received metformin, 850 mg twice daily throughout the cycle, and group 2 which includes 97 women who underwent laparoscopic ovarian drilling. If spontaneous ovulation or pregnancy was not achieved within 3 months after treatment, CC was added with increments of 50 mg (up to 150 mg/day) for both groups. Clinical and menstrual characteristics in addition to the hormonal profile were evaluated before and after the treatment. There were no significant differences between the two groups in terms of age, body weight, BMI, duration of infertility and serum hormone levels (androgens, gonadotrophins, insulin) before starting the treatment. A significant improvement in the regularity of menstrual cycles (P < 0.05) and a significant reduction in the serum levels of testosterone(P<0.01), androstenedione (P<0.01), DHEAS (P <0.05), LH (P<0.01) and LH:FSH ratio (P<0.05) were noted after the treatment. There were no significant differences between the metformin group compared with the drilling group in the rates of ovulation (79.7% vs. 83.5%) and pregnancy (64.1% vs. 59.8%). It is concluded that CC-resistant patients with polycystic ovary syndrome can be treated effectively either by metformin or by laparoscopic ovarian drilling. Menstrual cycle pattern and the rates of ovulation and pregnancy are improved significantly, due most probably to the significant decrease in the levels of androgens and luteinising hormone.