Background: Polycystic ovarian syndrome is a common endocrine disorder affecting 6-10% of women of reproductive age and the most common cause of anovulatory infertility. Objective: The aim of the study was to compare the effectiveness, side effects and outcomes of step-up gonadotrophin protocol versus laparoscopic ovarian diathermy (LOD) in infertile patients with clomiphene citrate resistant polycystic ovary syndrome. Methods:  The sample included women who attended our infertility clinic at Al-Elwiya Maternity Teaching Hospital and Kamal Al-Samarraee for Infertility and IVF Hospital in Baghdad/ Iraq from November 2013 to November 2014.    Eighty cases of infertile women with polycystic ovarian syndrome who failed to ovulate with clomiphene citrate for six months where collected, forty women treated with step-up protocol with low dose recombinant FSH gonadotrophin which increased gradually according to ovulation response, another forty women treated with LOD. Ovulation monitoring in each group was done with transvaginal ultrasound to exclude monofollicullar, bifollicular ovulation, ovarian hyperstimulation syndrome, multiple pregnancy and pregnancy rate in each cycle for 6 cycles. Results: Higher unifollicular ovulation and pregnancy rate in LOD than step-up protocol (91.4% & 25% versus 75% & 10%) respectively, while multifollicular and hyperstimulation rate were higher in gonadotrophin group (24.3% & 0.1% versus 8.50% & nil) respectively. Conclusion: Ovulation induction and pregnancy rate per cycle was higher with LOD group, not time consuming, also there was no risk of hyperstimulation of the ovary or twin pregnancy as compared to the step-up protocol with gonadotrophin