Introduction: One of the causes of infertility is anovulation due to polycystic ovary syndrome (PCOS). In women with PCOS, Elevated serum LH levels and an increased ratio of LH to FSH is generally seen. To prevent an increase in LH and follicular atresia, the use of FSH is proposed. The aim of the present study was to compare pregnancy rate of two regimens of recombinant FSH (r-FSH) and urinary FSH (u-FSH) in patients with PCOS under IUI.Methods: This is a descriptive- analytical (retrospective) study which conducted on 441 infertile women with PCOS that referred to infertility clinic of Kashan Shahid Beheshti Hospital (in two years), and met the inclusion criteria for the study; the data was collected by referring to patients’ files.Results: there was no significant difference between the two groups in the mean endometrial thickness, number of dominant follicles, gonadotropin consumption, duration and type of infertility. Pregnancy rates in patients treated with the u-FSH was 6.28% and in the patients treated with r-FSH was 9.30%, and the difference was not statistically significant (P=0.59).Conclusion: The results of this study showed that the there is no difference in terms of pregnancy rate between two products, u-FSH and r-FSH, in infertile patients with PCOS under IUI. Therefore, we can use both of these products according to availability, cost and patient acceptance.