To compare two gonadotropin-releasing hormone agonists for down-regulation prior to superovulation in in vitro fertilization/embryo transfer treatment. Infertility patients (n=181) were randomized to receive buserelin (1200 microg/day, n=90) or nafarelin (800 microg/day, n=91) intranasally starting in the luteal phase. Serum levels of LH, estradiol and progesterone were measured during the treatment. The cycles were compared with regard to number of oocytes, fertilization and implantation rates and achieved pregnancies. Serum LH was lower after two weeks on buserelin: 1.8 (1.3-2.4) IU/L (median, with lower and upper quartile in parenthesis), than after nafarelin: 2.6 (1.8-4.0) IU/L, (p=0.0001). No other differences in serum hormone levels could be detected. More oocytes were recovered in the buserelin group: 13.0 (8.0-19.0) vs 11.0 (6.8-15.0), (p=0.046), but the fertilization rate was higher in the nafarelin group (49.9%, vs 45.1%, p=0.023). Implantation rate was higher in the nafarelin group (26.28% vs 15.5%, p=0.030), but there were an equal number of deliveries in both groups (20.9% vs 15.6% per started stimulation, p=0.420). In the subsequent frozen-thawed embryo transfer cycles the implantation rate was 21.1% (nafarelin group) and 10.6% (buserelin group, p=0.067), the pregnancy rate/ET was 31.7% and 17.0% (p=0.107) and the delivery rate was 22.0% and 10.6% (p=0.148), respectively. Differences exist in IVF-cycles down-regulated with buserelin or nafarelin which might affect embryo quality and treatment outcome.