Abstract Study question Is there any difference in the euploidy rate in a large cohort of blastocysts when produced after a progestin-primed or GnRH antagonist protocol? Summary answer Euploidy rates in trophectoderm biopsies when tested with next-generation sequencing (NGS) were similar after progestin-primed or GnRH antagonist protocol. What is known already Preimplantation genetic testing (PGT) might be employed in patients with advanced female age to improve efficiency of embryo transfer. Given the fact that there is no fresh embryo transfer in that policy, progestin primed ovarian stimulation (PPOS) protocol might be preferred over GnRH analogs due to its lower cost and advantage of oral administration instead of s.c injections. However, due to small sample sizes within the limited number of studies, there is lack of consensus whether ploidy status might be affected when an embryo is generated after a PPOS or GnRH analogs protocol. Study design, size, duration A retrospective cohort study was designed among patients that has undergone in-vitro fertilization (IVF) treatment between January-2018 and June-2023 in Bahceci Health Group. For the aim of PGT, only patients treated with PPOS or GnRH antagonists were included. PPOS protocol referred to utilization of either medroxyprogesterone acetate (10 mg/day) or dydrogesterone (20-30 mg/day) to avoid premature ovulation during ovarian stimulation. In GnRH antagonist protocol, flexible or fixed approach was preferred for pituitary suppression. Participants/materials, setting, methods During the study period, 11.616 and 2.480 trophectoderm biopsies had been performed from blastocysts (D5/6) generated after GnRH antagonist or PPOS protocol, respectively. Of them, 9.390 and 1.801 of them were analyzed with NGS. A total of 303 (3.2%) and 17 (0.9%) biopsies were excluded due to failure or non-informative results after testing. For the final analysis, 9.087 and 1.784 biopsies were included in the antagonist and PPOS arms for the current study. Main results and the role of chance The mean age of women treated with GnRH antagonist and PPOS was comparable (36.5±5.3 vs. 36.7±5.4 years, p = 0.17). The respective numbers of euploid embryos were 3.912 and 1.784. Per biopsied embryos, the rate of euploidy was 33.7% and 34.8% (p = 0.30). The rate of euploidy per metaphase II oocyte and 2-PN were 10.6% and 13.5% in the GnRH antagonist arm and they were 11.3% and 14.4% in the PPOS arm (p = 0.08 and p = 0.07) without any statistical significance. When only patients included in whom all available blastocysts were biopsied, the linear regression model revealed only female age (RR: -0.32 CI%95: -0.38 to – 0.26, p < 0.001) as the independent factor for the prediction of ploidy rate (euploid/euploid + aneuploid embryos) when body mass index, duration of infertility, AMH, number of oocytes, number of metaphase-II oocytes, and the type of ovarian stimulation protocol were entered into the model. This model represented female age as the sole independent factor (RR: -0.14 CI%95: -0.18 to – 0.11, p < 0.001) when euploidy rate per 2PN was tested with the same variables. Limitations, reasons for caution The inherent risks cannot be excluded due to the retrospective nature of the current study. Wider implications of the findings The current study includes the largest number of trophectoderm biopsies generated from PPOS and GnRH antagonist protocol, giving the opportunity to compare them with each other. Due to lack of any superiority of one protocol regarding ploidy status, financial cost and easiness might favor PPOS when PGT is planned. Trial registration number None