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Objective: To compare the effectiveness of letrozole and clomiphene citrate (CC) on uterine blood flow rate in patients with unexplained infertility. Materials and methods:In this randomized clinical trial 90 women with unexplained infertility referred to a university clinic from January 2011- December 2013 were enrolled. Thirty patients were randomized for letrozole, 30 patients for CC and 3o patients for control group. On the day 3 of cycle the patients were given letrozole 2.5mg/day or CC 100 mg /day orally or did not receive any treatment. Resistance index (RI) and pulsatility index (PI) of uterine artery were calculated and chemical pregnancy rate was evaluated. Results:Mean age was 26.4±3.2 (20-33) and mean BMI was 26.3± 3.2. After treatment using ultrasonography the Resistance index (RI) and Pulsatility index (PI) showed no significant difference among three groups (P > 0.05). Pregnancy rate in letrozole group (58%) was more in comparison to CC (53.6%) and control groups (46%) but the difference was not significant (P > 0.05). Conclusion: Our study showed that letrozole and clomiphene citrate have comparable impact on uterine blood flow and pregnancy rate in women with unexplained infertility.