Abstract Study question Does multinucleation at the two-cell stage significantly affect pregnancy outcomes, and how does it differ between day 3 and day 5 embryo transfers? Summary answer Multinucleation at the two-cell stage has a negative effect on pregnancy outcomes in day 3 embryo transfers, but not in day 5 transfers. What is known already Time-lapse imaging provides a valuable tool to study multinucleation in human embryos, although the impact on development and pregnancy remains debated. Literature shows conflicting findings, with most studies associating multinucleation in the early stage embryo with altered developmental potential and decreased pregnancy outcomes. However, other studies suggest a positive correlation, indicating that multinucleated embryos can progress successfully through development and lead to positive pregnancy outcomes. These discrepancies underscore the complexity of and highlight the need for understanding the implications of multinucleation in the context of human embryo development and pregnancy. Study design, size, duration A non-interventional retrospective study on multinucleation was performed on all cycles cultured in a time-lapse incubator in a Dutch fertility clinic between November 2021 and July 2023. In total, 915 embryos (out of 406 cycles) were analyzed and 406 resulting transfers (both fresh and frozen-thawed) were included in this study. Participants/materials, setting, methods Fresh single-embryo transfer was performed on day 3 (for cycles with less than 4 2PN-embryos) or day 5 (for cycles with 4 or more 2PN-embryos). Embryos were vitrified on day 5 or 6 (at least B3BB Gardner score). Nucleation status at the two cell stage was annotated for all transferred and vitrified embryos. Ongoing pregnancies were compared for embryos with or without multinucleation (mononucleation) at the two cell stage. Main results and the role of chance Multinucleation at the two cell stage was observed in 40% (n = 366/915) of all embryos. Multinucleated embryos transferred on day 3 showed a decreased ongoing pregnancy result (17%; n = 9/54) compared to the mononucleated day 3 transfers (29%; n = 24/83). For day 5 transfers, no difference in ongoing pregnancy rates was observed between the multinucleated (37%; n = 37/101) and mononucleated (37%; n = 62/168) groups. These results indicate that development to the blastocyst stage negates any possible negative effect multinucleation can have on cleavage stage embryos. Limitations, reasons for caution A mayor limitation to this study is the small sample size of specifically day 3 transfers. Patients with more than one transfer were allowed to be included. Confounding factors were not assessed. Additionally, different types of multinucleation might result in different clinical effects. Wider implications of the findings Although additional research is needed, these results suggest that assessment of nuclear status at the two-cell stage is important for day 3 transfer strategies, but less so for day 5 blastocyst transfers. Trial registration number Not applicable