The aim of this study was to compare the incidence of ectopic pregnancy in GnRH agonist triggered IVF cycles with intensive luteal support versus hCG triggered IVF cycles. This study was conducted as a retrospective cohort analysis of women who underwent IVF treatment employing GnRH agonist or recombinant hCG (rhCG) triggers during 2-year period. The medical charts of women who achieved pregnancies were reviewed and their demographic characteristics, infertility reasons and IVF data were recorded. A multiple logistic regression analysis was performed to estimate the association between the triggering medication used to stimulate final oocyte maturation (GnRHa or rhCG) and EP, with adjustment for important confounders: the day of embryo transfer (ETD), the etiology of infertility and estrogen level at the time of triggering. The number of metaphase II oocytes, fertilized oocytes and good quality embryos were significantly higher in the GnRH agonist triggered group compared with the hCG triggered group (p < 0.001 for all). The clinical pregnancy and implantation rates in the hCG triggered cycles were 38.6 and 31.1 %, respectively and 24.7 and 22 %, respectively in the triptorelin triggered cycles. The ectopic pregnancy rates were 5.3 % in the triptorelin triggered group and 1.4 % in the hCG triggered group. The trigger medication and the day of embryo transfer were found to have a significant effect on the probability of developing ectopic pregnancy (p = 0.028, p = 0.046 respectively). However, the estrogen level was not found to have a significant effect on the probability of developing ectopic pregnancy (p = 0.447). The reasons for higher ectopic pregnancy rates in GnRH agonist triggered cycles relative to hCG triggered cycles may be the decreased receptivity of the endometrium due to insufficient luteal support and higher implantation potential of embryos in correlation with a higher number of good quality embryos obtained in these cycles.