Abstract Study question What frozen-thawed embryo transfer (FET) protocol is associated with the highest live birth rate (LBR)? Summary answer: Natural cycle FET (NC-FET), with or without hCG triggering are associated with higher LBR and clinical pregnancy rate (CPR) compared to artificial HRT-FET cycles. What is known already FET cycles (as opposed to fresh ET) are now the most frequently performed treatment in ART. There are many reasons for this including better laboratory cryopreservation techniques, increased single ET cycles, freeze-all cycles to reduce OHSS, as well as PGT-A and personalized ET. Nevertheless, there is no clear consensus on the most effective protocol. Study design, size, duration Retrospective cohort study with FET of cleavage (n = 220) and blastocyst (n = 3258) embryos thawed 2013–2018 in a single academic center. FET protocols were NC-FET (n = 182), artificial HRT-FET (n = 3159) and modified NC (mNC) with hCG triggering (n = 137). Other cycles (gonadotrophin or GnRH agonist) and women with uterine anomalies were excluded. Primary outcome was LBR. Secondary outcomes were CPR, visits per cycle and endometrial thickness. Adjustment was made for potential known confounders. Participants/materials, setting, methods In NC-FET, no medication was given and ET timing was by serum LH surge. In mNC-FET, hCG was given when the lead follicle reached 18mm rather than awaiting the LH surge. In artificial HRT-FET, estradiol valerate was given and once endometrial thickness reached 8mm, progesterone was added and ET was planned. Adjustment for female age at oocyte retrieval, embryo stage, embryo grade, year of freezing, year of thawing, infertility cause and endometrial thickness was performed. Main results and the role of chance There were no significant differences between the groups with regard to female age at oocyte retrieval, embryo stage, embryo grade, embryo number, cycle number and endometrial thickness. As expected, more women with irregular cycles were included in the artificial HRT-FET compared to NC-FET (16.1% vs. 8.2%, p = 0.003) and mNC-FET (16.1% vs. 4.1%, p < 0.0001). There were more visits per cycle in NC-FET and mNC-FET compared to artificial HRT_FET (p < 0.0001). LBR was higher in the mNC-FET (38.0%) and NC-FET (31.9%) compared to artificial HRT_FET (20.2%) (p = 0.0001 and p = 0.0003 respectively). CPR was higher in mNC-FET compared to artificial HRT-FET (45.3% vs. 32.3%, p = 0.0002), and in NC-FET compared to artificial HRT-FET (44.5% vs. 32.3%, p = 0.0009). There was no significant difference in LBR or CPR between NC-FET and mNC-FET. Sub-analysis of the first FET showed similar results. Biochemical pregnancy loss and miscarriage rates were similar in all groups. The higher LBR with NC-FET and mNC-FET remained significant even after adjusting for potential confounders, (aOR 2.42, 95%CI: 1.53–3.66, p < 0.0001). Limitations, reasons for caution The interpretation of the findings of this study is limited by the retrospective nature of the analysis and the potential for unmeasured confounding variables. Wider implications of the findings: Although artificial HRT FET cycles are more common, convenient and practical for clinicians, with less visits per cycle, its use must be cautiously reconsidered in light of the potential negative effect on LBR when compared with natural cycle FET. Trial registration number Not applicable