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Background and Objective: Infertility and its treatment is one of the most important challenges that gynecology faced it. This study compares two methods of administration of GnRH agonists and GnRH antagonists on the occurrence of pregnancy. Materials and Methods:  This study is a randomized controlled clinical trial. 84 infertile couples with male factor infertility problems referred to Fatemieh Hospital of Hamadan were enrolled in this study and randomly assigned to two groups of 42 cases, the first group treated with agonist GnRH (Bucereline) and the second one treated with GnRH antagonists (Cetrotide). Two groups regarding the incidence of pregnancy, number of oocytes obtained, the average days of induction and the number of fertilized oocytes, the incidence of OHSS syndrome and treatment costs were compared. Results: Findings showed that the clinical pregnancy rate in the agonist group, 19 cases (45.23%) and the antagonist group, 7 cases (16.67%) has been observed. The difference was statistically significant (P<0.009). Number of fertilized oocytes in agonist group was significantly higher than antagonist (P<0.004) and the average induction days in the antagonist group was significantly lower (P<0.001). The difference between incidence of OHSS syndrome and the overall cost of treatment in both groups was not significant. Conclusion: We suggested  that the efficacy of agonist drugs in occurrence of pregnancy are much better than antagonist drugs even though the complications do not differ in both groups.