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Freebase (0.00 / 0 votes) Rate this definition: Blastocyst. The blastocyst is a structure formed in the early gestation of vertebrates. It is preceded by the morula. It possesses an inner cell mass, or embryoblast, which subsequently forms the embryo, and an outer layer of cells, or trophoblast, surrounding the inner cell mass and a fluid-filled cavity known as the blastocoele. The human blastocyst comprises 70-100 cells.