Background: Clomiphene citrate is the most popular drug for ovulation induction mainly in cases of PCOS, used alone or with combination of other drugs e.g. metformin. Aim: To evaluate the efficacy of stair step protocol versus traditional protocol using clomiphene citrate alone or combined with metformin and to assess the uterine and systemic side effects of cumulative doses in single cycle. Patient and Methods: Sixty (60) patients in two groups diagnosed as PCOS, based on the revised Rotterdam criteria (2003), *Group 1: In the stair-step protocol (n = 30), Clomiphene Citrate was administered at 50 mg daily for 5 days following the onset of a spontaneous or progestin- induced menses. The follicular response monitored by TVS starting on day 8. When the mean diameter of the follicle size is below 11mm on cycle day 14, the dosage increases to 100 mg/day for 5days.Then on cycle day 19 re-evaluation by TVS was restarted. Metformin with initial dose 500mg/day (and gradually increased to 1,500 mg /day during 6 weeks).**Group 2: In the traditional protocol (n = 30), Clomiphene citrate was administered 100 mg daily for 5 days after the onset of spontaneous or progestin-induced menstruation. The following variables were measured: ovulation rate (The number of follicles that mature and ovulate during given menstrual cycle), Side effects on uterine artery & systemic side effects e.g. Hot flushes. Results: The findings of this study indicated no significant difference between the 2 groups in using clomiphene citrate by stair step protocol or traditional protocol (P>0.05). Conclusion: Clomiphene citrate in the stair step protocol combined with metformin has a higher efficacy compared to CC in the traditional protocol in patients with PCOS in terms of ovulation and clinical pregnancy rates without any detrimental side effects on endometrial thickness or Doppler of uterine arteries, stair step protocol suitable for use in clinical practice.