The purpose of the present study was to determine whether the presence of one or more multinucleated blastomeres during early embryonic development is associated with chromosomal abnormalities in sibling blastomeres of that embryo. Embryos with multinucleated cells (n = 47) detected on day 2 or 3 or development were compared to dividing embryos without multinucleation. Arrested embryos were excluded from this study. Chromosome abnormalities were detected using fluorescent in-situ hybridization (FISH) with X, Y, 18 and 13/21 chromosome-specific probes. Of 47 embryos included in this study, 76.6% were chromosomally abnormal, compared to 50.9% in the control group (P < 0.001). Excluding aneuploidy, which is originated in the gametes and not the embryo, the differences were even higher, with 74.5% of multinucleated embryos being chromosomally abnormal compared to 32.3% of non-multinucleated embryos (P < 0.001). Day of multinucleation appearance, number of nuclei per cell, number of multinucleated cells per embryo and developmental quality of the embryos as well as the type of fertilization (intracytoplasmic sperm injection versus standard insemination) were not found to affect the rate of chromosomal abnormalities in embryos with multinucleated cells. These results suggest that embryos with multinucleated cells may not be suitable for replacement and should be excluded unless no other embryos are available.