OBJECTIVE The objective was to evaluate the relationship between ploidy and chromatin status of human unfertilized oocytes/zygotes and infertility history, female age, and stimulation regimens. METHODS Two hundred and eighty-nine unfertilized oocytes and 63 zygotes were subjected to cytogenetic analysis: karyotyping for oocytes and fluorescent in situ hybridization (FISH) analysis for zygotes. Ploidy and chromosome/chromatin status were analyzed according to stimulation regimen, female age, and infertility history. The correlation coefficient was estimated and data were interpreted using a five-grade scale. RESULTS Aneuploidy in karyotyped oocytes (19.7% hyperhaploidy, 18.8% hypohaploidy, and 6.3% haploid abnormal) was associated with chromosome fragmentation and lesions due to chromosome aging in culture. Premature chromosome condensation and cytoskeletal defects were significantly higher in unexplained infertility (34.7% and 52.9%, respectively; p<0.05). Chromatin quality was most important for successful ploidy analysis of zygotes. FISH analysis of abnormal zygotes elucidated genetic aspects of pronuclear number aberrations and raised questions about the current selection criteria. Abnormalities were found to correlate moderately with stimulation strategy and female age and significantly with infertility history. CONCLUSIONS Genetic analysis of human oocytes and zygotes showed that poor chromatin quality and patient-related factors contribute to aneuploidy and pronuclear number aberrations.