This study investigated the effect of vitrification on biopsied embryos at various developmental stages. After biopsy on day 3, embryos were vitrified at cleavage, morula and blastocyst stages using a commercially available kit. Nonbiopsied embryos were vitrified as controls. For day-3 cleavage embryo vitrification, embryos from abnormally fertilized oocytes were randomly allocated to the biopsy and control groups. For morula and blastocyst vitrification, the embryos used in the biopsy groups were obtained from aneuploidy or affected embryos diagnosed by preimplantation genetic diagnosis (PGD). After warming, survival, blastulation and development of embryos in different groups were compared. The survival rate after warming in the non-biopsied cleavage control group was significantly higher than in the biopsied cleavage group (92.0% versus 64.0%, P = 0.037). Most of the biopsied embryos were destroyed due to blastomeres escaping. At the morula stage, both biopsied and non-biopsied embryos had similar survival rates. However, a significantly higher survival rate (95.6%) was observed in the biopsied blastocyst group compared with the control group (81.3%, P = 0.035). Biopsied embryos vitrified at an advanced stage had as high survival rates as non-biopsied embryos. Vitrification at the blastocyst stage is a practical and efficient solution for embryo cryopreservation during PGD.