The anterior portion of the endodermal gut, lying immediately posterior to the mouth cavity, expands laterally as the pharynx. The lateral pockets of the pharyngeal cavity, called the pharyngeal pouches, perforate the mesodermal layer, reach the ectoderm, and break through to form pharyngeal, or gill, clefts. In fishes and larvae of amphibians, these clefts develop gills and become respiratory organs. Pharyngeal pouches develop in the early embryos of all vertebrates, including the air-breathing terrestrial reptiles, birds, and mammals. The number of pouches has been reduced in the course of evolution from six or more to four in tetrapods, and the posterior pouches may not actually break through.

The consistent development of pharyngeal pouches and clefts indicates their importance in vertebrate development. Many parts of the vertebrate body are derived from, or dependent on, the pharyngeal pouches; for example, the aortic arches—the most important blood vessels of a vertebrate—develop between successive pharyngeal pouches. Skeletal visceral arches also occur between consecutive pharyngeal pouches (they do not develop if the pharyngeal pouches are prevented from developing). In adult terrestrial vertebrates, parts of the visceral arches are transformed into the hyoid apparatus, supporting the tongue, the auditory ossicles, and parts of the larynx and trachea. Furthermore, some of the material of the pharyngeal pouches is utilized for the formation of the parathyroid glands and the thymus; the former are indispensable glands of internal secretion, and the latter are a source, in mammals, of cells that produce antibodies. The pharynx also produces the rudiment of the thyroid gland as a ventral outgrowth.

The liver, pancreas, and lungs

Three additional important organs develop from the endoderm: the liver, the pancreas, and the lungs. The liver develops as a ventral outgrowth of the endodermal gut just posterior to the section that eventually will become the stomach. Initially, the liver takes the form of a tubular gland, but it soon acquires a close relationship to the blood sinuses and capillaries, forming lobules around blood vessels rather than around glandular ducts. The pancreas develops from three independent rudiments: two ventral ones, formed just posterior to the liver rudiment, and a dorsal one. The ventral and the dorsal rudiments fuse in most vertebrates to form one organ with a complicated system of ducts opening into the duodenum, a portion of the small intestine. The lungs develop from a ventral hollow outgrowth of the gut, which is located just posterior to the pharyngeal region; the outgrowth branches into a right and left trunk that grow posteriorly beside the esophagus and then expand into hollow sacs, in lower terrestrial vertebrates, or into a system of tubes, in birds and mammals.

The endodermal parts of the alimentary system are, along their entire length, encased by the splanchnic mesoderm of the lateral plates. The coelomic cavities of the right and left sides fuse ventral to the gut but remain separated dorsally by their respective walls, which form the dorsal mesentery—a double membrane by which the gut is suspended from the dorsal side of the body cavity and through which blood vessels and nerves reach the gut. The layer of splanchnic mesoderm next to the endoderm produces the connective tissue and muscular layers of the gut. During development of the glands of the alimentary canal (e.g., pancreas, salivary glands), the mesoderm forms a connective tissue capsule around the branching tubules of the gland. The development of the tubules is dependent on this mesodermal capsule and cannot proceed without it.