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Purpose This retrospective cohort study determined the relative efficacy of blastocyst and cleavage-stage transfers in patients with differing numbers of zygotes. Methods A total of 1116 women whose embryo transfers were planned independently of patient characteristics were included. Cleavage-stage (D3) and blastocyst-stage (D5) transfer outcomes were analyzed per number of zygotes. The D5 group included transfer cancellations as the intention-to-treat population. The effect of the embryo transfer date on the clinical outcomes (clinical pregnancy and implantation rates) was analyzed using multivariate logistic regression. Results Among the patients, 584 and 532 underwent D3 and D5 embryo transfers, respectively. The clinical pregnancy rates were significantly higher in D5 patients with ≥ 6 zygotes (25.7% vs 48.3%). The multivariate logistic regression analysis for clinical pregnancy did not show significant differences between the blastocyst and cleavage-stage transfers in patients with ≤ 5 zygotes (0.874). Compared to the cleavage-stage, blastocyst-stage transfers for patients with ≥ 6 zygotes resulted in a three-fold increase in clinical pregnancy rates (3.122). Conclusion Blastocyst transfers were not inferior to cleavage-stage embryo transfers among patients with few zygotes and were preferable for patients with several zygotes.