The objective of this study was to describe the ultrastructure of blastocysts derived by in vivo and in vitro methods and to investigate how the morphology is affected by exposure to cryoprotectant (10% glycerol) or cryopreservation by conventional slow freezing. In vivo derived blastocysts were characterized by a narrow perivitelline space (PvS), a continuous cover of numerous stacked microvilli (MV) on the plasma membrane, a well-defined system of cell-to-cell coupling and a large population of round or elongated mitochondria with numerous transverse cristae. Exposure of these blastocysts to cryoprotectant was manifested by shrinkage of the blastocysts and swelling of the mitochondria. Cryopreservation resulted in further shrinkage, damage to the MV, and accumulation of cellular debris. In comparison, the in vitro matured (IVM)/in vitro fertilized (IVF) in vivo cultured blastocysts displayed a wider PvS; they appeared to possess less MV and all blastocysts displayed some cellular debris in their PvS. There was also a decrease in the number of junctional contacts between the trophoblastic cells. The reaction of these blastocysts to exposure to cryoprotectant was similar to that of the in vivo derived blastocysts. However, they appeared to be more susceptible to cryopreservation. The totally in vitro produced (IVP) blastocysts displayed a wider PvS, no stacking of the MV, increased numbers of lipid droplets and a further reduction in the junctional contacts between trophoblastic cells. The IVP blastocysts sustained breakage of the zona pellucida on exposure to cryoprotectant and were extremely sensitive to cryopreservation, losing all cell structure and organization. The findings of the present study indicate that in vivo derived blastocysts possess certain structural characteristics that confer a greater tolerance on them to exposure to cryoprotectant and cryopreservation.