In-vitro generated human embryos have low implantation rates and high chromosomal abnormalities. Embryos are mostly selected on the basis of microscopic morphological examination. The relationship between pronuclear morphology and chromosomal abnormalities was investigated in this study. Zygotes were scored according to pronuclear morphology on day 1. Excess embryos that were not transferred or cryopreserved on day 3 were fixed. Chromosomes 13, 18, 21, X and Y were analysed by fluorescence in-situ hybridization (FISH). A total of 125 embryos were analysed; 58 (46%) were abnormal, 32 (26%) were mosaic and 35 (28%) were normal. Results were analysed according to different pronuclear morphology. Zygotes with polarized pattern had a significantly lower incidence of chromosome abnormality than those with a non-polarized pattern. The presence of cytoplasmic halo, the size of each pronucleus and the number of nucleolar precursor body had no significant effect on chromosomal abnormalities. In conclusion, embryos generated from zygotes with polarized pattern have fewer chromosomal abnormalities compared with other patterns. A simple microscopic examination during fertilization confirmation would be useful to select embryos with fewer chromosomal abnormalities, preferably in combination with other observations shown to correlate with chromosomal abnormalities.