The quality of oocytes and developing embryos are the most relevant factors determining the success of an in vitro fertilization (IVF) treatment. However, there are very few studies analyzing the effects of different gonadotrophin preparations on oocyte and embryo quality. A retrospective secondary analysis of data collected from a prospective randomized study was performed to compare highly purified versus recombinant follicle stimulating hormone (HP-FSH vs. rFSH). The main outcome measures were quantity and quality of oocytes and embryos, dynamics of embryo development, cryopreservation, clinical pregnancy and live birth rate. The number of retrieved and of mature (MII) oocytes showed no significant differences. Fertilization rate was significantly higher in the HP-FSH group (68.9% vs. 59.9%, p = 0.01). We also found significantly higher rate of cryopreserved embryos per all retrieved oocytes (23.4% vs. 14.5%, p = 0.002) in the HP-FSH group. There were no significant differences in clinical pregnancy and in live birth rates. Oocytes obtained with HP-FSH stimulation showed higher fertilisability, whereas pregnancy and live birth rates did not differ between the groups. However, patients treated with HP-FSH may benefit from the higher rate of embryos capable for cryopreservation, suggesting that cumulative pregnancy rates might be higher in this group.