In amphioxus the digestive tract consists of only three components: the oral cavity, the pharynx, and a tubular postpharyngeal gut without subdivisions. The same condition holds in the most primitive living vertebrates, the cyclostomes (lampreys and hagfishes). In higher vertebrates, however, the postpharyngeal gut is almost always subdivided into a series of regions that are both anatomically and functionally distinct. The most common is the esophagus–stomach–small intestine–large intestine–rectum (or cloaca) sequence.

The oral cavity and pharynx vary considerably among the vertebrate classes. The variation correlates with the evolutionary changes in the respiratory system that accompanied the rise of terrestrial forms from aquatic ancestors. In most modern-day bony fishes, the nares (corresponding to a mammal’s nostrils) function only as entrances to the olfactory organs, there being no connection between them and the mouth, as occurs in mammals. The structure called the palate, which in mammals separates the nasal and oral cavities, does not exist in fishes. Respiratory water is taken directly into the mouth and then forced back into the pharynx, where it flows across gills located in a series of slits leading from the pharynx to the exterior.

The terrestrial vertebrates, which extract oxygen from air instead of from water, evolved a second major function for the nares that they inherited from their piscine ancestors. While retaining a smell function, these openings became the principal entrance of air for breathing. In amphibians—the earliest land vertebrates—air enters the external nares and then passes through the internal nares, which are evolutionarily newer openings, into the front of the oral cavity, from which it moves into the pharynx and then into the trachea. There being no palate, no separate nasal cavity exists in these animals; both the oral cavity and the pharynx are common passages for the digestive and respiratory systems.

In most reptiles and birds, a pair of longitudinal folds in the roof of the oral cavity forms a passage that leads air from the internal nares to the pharynx. Complete separation of nasal and oral cavities by a palate, however, is found only in crocodilians and in mammals. In mammals the bony, hard palate is supplemented posteriorly by a thick, membranous, soft palate.

In the evolution of terrestrial vertebrates, the pharynx has lost the gas-exchanging gills and has become a short passage linking the mouth to the esophagus and the trachea. The esophagus has elongated to join up with the stomach, which now lies within the abdomen.

Most vertebrates above the level of the cyclostomes have a stomach, though of various shapes and sizes (the exceptions are the chimaeras, lungfishes, and a few bony fishes). The length of the intestine varies greatly among vertebrates, and a number of features have evolved that increase the area over which absorption of digestive products can occur. Increasing length alone permits longer contact between the product of digestion and the mucosa. Other features of advantage include the lining of the intestine, which is thrown into numerous folds and ridges; the small, fingerlike outgrowths, called villi, that cover the entire surface of the mucosa; and the individual epithelial cells that cover the folds and villi and have a border of countless closely packed, cylindrical projections called microvilli.

Other vertebrates show other adaptations for increasing the absorptive surface area of the small intestine. For instance, special blind sacs, called ceca, branch from the anterior end of the small intestine in certain fishes and from the posterior end in many birds. Another adaptation is the spiral valve of many primitive fishes, including sharks.

The final chamber of the digestive tract is a common cloaca in elasmobranch fishes and in lungfishes, but in most ray-finned fishes there is a rectum instead; i.e., the urinary and reproductive tubes, which do not join the digestive tube, have their own separate opening to the exterior. In this regard, then, the modern-day ray-finned fishes are more specialized than amphibians, reptiles, and birds, which retain a cloaca, presumably inherited from a primitive fish ancestor. A cloaca is also retained in the egg-laying mammals (monotremes) and, in a much-reduced form, in the pouched mammals (marsupials). Even in placental mammals a short-lived cloaca appears in the embryo, but the urogenital ducts eventually develop their own openings; as a consequence, mammalian adults have a rectum rather than a cloaca.