Background: We performed this study to investigate and compare the effects of Letrozole and gonadotrophins versus Clomiphene Citrate and gonadotrophins in women undergoing superovulation for Intrauterine Insemination (IUI). Methods: We performed this prospective cohort study at Australian Concept and Fertility centre, Karachi Pakistan. Women younger than 40 years of age with patent fallopian tubes and infertility of more than 2 years in duration who were undergoing IUI and gonadotrophins therapy were divided into two groups, one received Letrozole for 5 days and another received Clomiphene Citrate for 5 days. Results: All 500 IUI treatment cycles conducted from March 2008 to March 2010 were included. Patients co-treated with Letrozole required fewer gonadotrophins administrations (median difference, 300 IU (95% confidence interval (CI), 225-375 IU), developed more follicles larger than 14 mm (median difference, 1 follicle, 95% CI, 1-2 follicles), and had a thicker endometrium (median difference, 1 mm, 95% CI, 0.4–1.6 mm). The pregnancy rate was not significantly different between two groups (11% vs. 12.6%). Conclusion: The addition of Letrozole to gonadotrophins decreases gonadotrophins requirements and improves endometrial thickness, without a significant effect on pregnancy rates. An improved pregnancy rate has been observed in older age group, >35 years with Letrozole.