In the present study, we have carried out a comparative analysis of molecular karyotypes of cell free DNA from blastocoele fluid, trophectoderm and inner cell mass of human blastocysts at the preimplantation stages of development, using the comparative genomic hybridization. Different types of chromosomal abnormalities distribution between trophectoderm, inner cell mass and blastocoele fluid were identified. It was first shown that the source of cell free DNA in the blastocoele fluid may arise from the cells of inner cell mass in addition to the trophectoderm cells, which are traditionally used in preimplantation genetic diagnosis of chromosomal aberrations. These results support the promising of blastocentesis as a new technology of preimplantation genetic diagnosis, which provides the possibility of integral analysis of chromosome abnormalities in different cells of the blastocyst.