Protocol flexibility in PCOS: a combination of controlled ovarian stimulation and endometrial preparation strategies shows no impact on live birth outcomes after frozen embryo transfer—a retrospective cohort study

Objectives This retrospective study compares pregnancy outcomes in polycystic ovary syndrome (PCOS) patients across different controlled ovarian stimulation (COS) protocols—specifically GnRH antagonist and GnRH agonist cycles—combined with various frozen embryo transfer(FET) preparation methods, such as hormone replacement therapy (HRT) and ovulatory cycles. Despite the known variations in COS and FET protocols, the optimal combination for improving pregnancy outcomes in this population remains unclear.Methods We analyzed the first FET cycles of 2510 patients with PCOS at our center between January 2017 and September 2024. Baseline characteristics and pregnancy outcomes were compared using the Kruskal‒Wallis test, the chi-square (χ²) statistic, the Bonferroni correction for multiple comparisons, and inverse probability of treatment weighting (IPTW) adjustment.Results After IPTW adjustment, no significant differences were observed in live birth rates or other key reproductive outcomes among the four protocol combinations (all P > 0.05). Exploratory analyses revealed nonsignificant trends, suggesting two patterns: 1) GnRH agonist (vs. antagonist) COS protocols were associated with lower point estimates for the risks of preterm PROM and HDP; 2) ovulation (vs. HRT) cycles for FET preparation were similarly associated with lower point estimates for these risks.Conclusions For PCOS patients, live birth success is equivalent regardless of COS/FET protocol combination, supporting flexible treatment personalization. Clinical decision-making involves a critical trade-off: GnRH agonist protocols and ovulation FET cycles may be associated with a trend toward lower obstetric morbidity, potentially linked to the promotion of a more physiological ovulatory milieu. This balance between immediate iatrogenic risk and long-term pregnancy health warrants further study.