Gastrulation begins when a small indented crease, the dorsal lip of the blastopore, appears on one side of the blastula. The crease is formed by cells changing shape and pushing inward from the surface (invagination). Additional cells then roll inward over the dorsal lip (involution) and move into the interior, where they will form endoderm and mesoderm. Meanwhile, cells of the animal pole, the future ectoderm, change shape and begin spreading over the outer surface.

The blastopore lip grows on both sides of the embryo, as more cells invaginate. When the sides of the lip meet, the blastopore forms a circle that becomes smaller as ectoderm spreads downward over the surface. Internally, continued involution expands the endoderm and mesoderm, and the archenteron begins to form; as a result, the blastocoel becomes smaller.

Late in gastrulation, the endoderm-lined archenteron has completely replaced the blastocoel and the three germ layers are in place. The circular blastopore surrounds a plug of yolk-filled cells.