The notochord is a cylindrical column of cells that appears early in embryonic development. The notochord forms on the dorsal side of the embryo and establishes a bilateral longitudinal axis of development before the formation of the neural tube and spinal vertebrae. The formation of the notochord is a common and uniting factor of all chordate animals. In humans, cells forming the notochord later become part of the vertebrae, nasopharynx, and skull.

In the early developmental stages of all vertebrates, a notochord forms within the embryonic disk. The notochord lies between the ectoderm and endoderm. The rod of cells forms between the primitive knot and the prechordal plate of cells.

As mesoderm forms, aggregations (clumps or blocks) of cells, derived from mesoderm, form somites along the sides of the notochord. Depending on their level these mesodermal somites ultimately develop into vertebra, ribs, muscles, and dermal structures.

Formation of the notochord is critical to the proper formation and organization of the neural plate, neural folds, and subsequent development of the brain and other neural structures. One of the classic experiments in developmental biology, the organizer experiment, showed that in amphibian embryos, cells taken from the notochordal region of one embryo could induce neural structure formation when grafted on to a second embryo.