INTRODUCTION The aim was to compare the efficacy of long-acting and short-acting gonadotropin-releasing hormone (GnRH) agonists by long protocol on embryo quality, endometrial thickness and pregnancy rate in in vitro fertilization. MATERIAL AND METHODS In this retrospective study, long-term pituitary downregulation, achieved with long- and short-acting GnRH agonists (GnRHa), was performed for patients undergoing in vitro fertilization (n = 175). RESULTS There were no significant differences between the long and short-acting GnRH group (63.16% vs. 66.26%, p > 0.05), and the secondary and primary infertility group (63.47% vs. 66.86%, p > 0.05) in embryo quality. Logistic regression analysis showed that type of infertility and endometrial thickness were significantly associated with pregnancy outcome. Patients in the long-acting GnRHa group had a thicker endometrium on the day of human chorionic gonadotrophin (hCG) administration (10.79 ±2.62 mm vs. 9.64 ±1.97 mm, p < 0.01), lower serum luteinizing hormone (LH) concentration (1.21 ±1.13 vs. 2.53 ±3.39) and a higher pregnancy rate (59.60% vs. 43.42%, p < 0.05) than those of patients in the short-acting GnRHa group. CONCLUSIONS This work suggests that types of agonist protocol and infertility may not affect embryo quality. Type of infertility and endometrial thickness may be positive predictors for clinical pregnancy, but the key finding is that the long-acting GnRHa protocol may be an effective method of improving endometrial thickness, endometrial receptivity and pregnancy rate in in vitro fertilization.