The aim of this study was to determine whether follicular oestradiol and vascular endothelial growth factor (VEGF) concentrations in women with polycystic ovarian syndrome (PCOS) differ according to the use of gonadotrophin-releasing hormone (GnRH) antagonists or GnRH agonists. Furthermore, the effect of follicular oestradiol and VEGF concentrations on oocyte and embryo quality was investigated. In this prospective clinical study, 20 women with PCOS undergoing intracytoplasmic sperm injection for male factor infertility were included using a GnRH antagonist or a GnRH agonist protocol. In each follicle, oestradiol and VEGF concentrations were determined. In the GnRH antagonist group 254 follicles and in the GnRH agonist group 245 follicles, were aspirated. Fewer metaphase II (MII) and more immature and degenerative oocytes were registered in the GnRH antagonist group. Follicular oestradiol and VEGF were lower in the GnRH antagonist group (P = 0.014 and P < 0.001, respectively). Moreover, higher oestradiol concentrations were related to embryos of higher quality (P = 0.037). It is concluded that GnRH antagonists decrease follicular oestradiol and VEGF concentrations and the number of retrieved MII oocytes in women with PCOS.