To demonstrate chromosomal injuries associated with in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI), sister chromatid exchange (SCE), an indicator of DNA damage, was investigated and the cytogenetic influence of embryonic manipulation on chromosomes of early embryos and offspring was investigated. SCE analysis was performed in early embryos and offspring obtained by IVF, ICSI, or in vivo fertilization (control). To label chromosomes of early embryos, the embryos were cultured in BrdU-supplemented medium for 2 cell cycles. For offspring, BrdU solution was repeatedly injected intraperitoneally. Chromosome samples prepared from the embryos and the bone marrow cells of offspring were stained by the Fluorescence plus Giemsa (FPG) method. In the IVF and ICSI groups, the rates of early development, implantation and offspring were lower than those in the control group. The SCE frequency of early embryos was significantly higher in the IVF and ICSI groups than in the control group (P < 0.05). In contrast, the SCE frequency of offspring in the IVF and ICSI groups was not significantly different from that in the control group. These findings suggest that embryos having serious DNA damage due to embryonic manipulation may be eliminated in a relatively early developmental step and may not reach term.