In this randomized controlled trial, we aimed to examine whether differences exist among patients who underwent assisted reproductive technology treatment with a long-GnRH-agonist compared to a GnRH-antagonist protocol in terms of levels of follicular fluid (FF) and serum concentrations of vascular endothelial growth factor (VEGF), glycodelin and interleukin (IL)-1 beta on the day of oocyte pick-up (OPU). In 80 infertile couple with male factor or unexplained infertility, 40 women stimulated with GnRH-antagonist protocol and 40 women with the long-GnRH-agonist protocol. FF and blood serum samples were obtained simultaneously from 80 women during the OPU procedure and the concentrations of VEGF, IL-1 beta and glycodelin were measured with commercially available kits. Concentrations of FF VEGF, IL-1b and glycodelin were not significantly different in the long-GnRH-agonist and GnRH-antagonist groups, and neither were serum concentrations of VEGF, IL-1 beta and glycodelin. According to our results in at least, we can say that minor differences between these protocols in terms of clinical pregnancy do not depend on VEGF, glycodelin or IL-1 beta.