Background: The aim of the current study is to compare the efficacy of laparoscopic unilateral ovarian drilling with bilateral ovarian drilling in clomiphene citrate resistant cases of polycystic ovarian syndrome in terms of clinical response, change in biochemical parameters, ovulation rate, pregnancy rate and miscarriage rate.Methods: The study was conducted on 45 women with anovulatory infertility due to PCOS with clomiphene citrate resistance. By random selection, all patients were divided in two groups. In group 1, unilateral ovarian drilling was done and in group 2, bilateral ovarian drilling was done. A maximum of 5 drills were performed using insulated unipolar diathermy needle. Patients were followed up for one year and the clinical outcome in two groups were recorded and compared.Results: Post ovarian drilling it was seen that no major differences were noted between the two groups in return of spontaneous menstruation at 6 weeks (65% vs 60%), overall ovulation rate (55% vs 65%) and pregnancy rate (45% vs 40%). The mean fall in serum LH, serum FSH and serum testosterone were also similar in the two groups.Conclusions: Unilateral laparoscopic ovarian drilling had similar efficacy as bilateral laparoscopic ovarian drilling in terms of restoration of normal menstrual pattern, ovulation and achieving pregnancy. It is an effective alternative minimally invasive procedure for patients with resistant PCOS.