The mammalian gut has become highly specialised along its length to make digestion a quick and efficient process. The rapid digestion of complex food molecules is necessary to supply the mammal with the materials needed to generate the heat necessary to maintain a relatively constant body temperature.

The buccal cavity contains an array of teeth which are specialised according to the type of food eaten, they range from sharp needle like teeth of insect and fish eaters to the flat crushing and grinding teeth of herbivores. The teeth of many mammals mechanically digest the food to form small particles which gives the food a larger surface area allowing faster digestion by enzymes. The salivary glands produce saliva which contains sodium hydrogen carbonate, amylase, and mucus. This is mixed with the food and the tongue then pushes the food to the rear of the cavity where it touches the pharynx wall. Sense cells in the pharynx wall cause a swallowing reflex and stimulate waves of peristalsis which run down the oesophagus, pushing the food into the stomach through the relaxed cardiac sphincter muscle.

Once in the stomach the food is mixed with gastric juice secreted by the gastric glands in the stomach wall. The juice contains hydrochloric acid, pepsinogen and rennin. The acid alters the pepsinogen to form the active enzyme pepsin. Once formed the pepsin activates more pepsinogen by converting it into pepsin, a process called autocatalysis. Pepsin is an endopeptidase which is a protein digesting enzyme attacking the peptide bonds between the amino acids at points inside the protein chain. Rennin is a highly specific protease enzyme which converts milk protein caseinogen from a globular form into casein which is fibrous. This change in the milk protein causes the protein to coagulate forming solid clumps which are easier to digest. The hydrochloric acid provides the optimum pH for the action of pepsin and rennin to act as catalysts and also reduces the possibility of bacterial growth since the vast majority of bacteria cannot tolerate the low pH of the stomach. The gastric glands are tubular pits in the stomach wall which contain two main types of cell, the oxyntic cells and the chief or zymogen cells. The oxyntic cells secrete the hydrochloric acid and are found towards the top of the gastric glands. The zymogen cells secrete the enzyme precursors pepsinogen and prorennin, and are found lower down in the glands. Around the neck of the gastric glands where they open into the stomach space there are many mucus secreting cells. The layer of mucus in the stomach helps to prevent damage to the stomach wall itself from the acid and highly active enzymes. The stomach wall possesses three layers of smooth muscle, the outer longitudinal layer and inside this the circular layer which are both found in all areas of the gut and are responsible for peristaltic contractions, and inside of these is a spiral layer of muscle which give the stomach the ability contract in a spiral fashion. These muscles are constantly contracting in sequence to churn the food, thereby mixing it with the gastric juice and also mechanically digesting it into a semi-liquid sludge called chyme. The food is prevented from leaving the stomach by contraction of the upper cardiac and lower pyloric sphincter muscles.

The food is expelled from the stomach in small amounts by relaxation of the pyloric sphincter and it passes into the first section of the small intestine called the duodenum. The food is mixed with three digestive juices in the duodenum.

Bile juice, produced by the liver and stored in the gall bladder. It adds fat emulsifying bile salts but no enzymes. It also contains bile pigments, waste products derived from the dead red blood cells being recycled by the liver, these stain the food material a brown colour.

Pancreatic juice, produced by the pancreas, the pancreatic cells produce sodium hydrogen carbonate solution and the enzymes carbohydrase, lipase, nuclease, chymotrypsinogen and trypsinogen, the last two being inactive forms of exopeptidase and endopeptidase which are activated by enterokinase when they enter the gut space.

Intestinal juice, was once thought to contain digestive enzymes which completed the digestion of food molecules but it is now known to be an alkaline solution with few enzymes present, namely nucleotidase and enterokinase. The enzymes responsible for the final stages of food digestion are bound to the cell membranes of the intestinal epithelial cells and some are in their cytoplasm.

Absorption of food by the small intestine occurs along the length of the ileum. The lining of the ileum has thousands of tiny finger like projections called villi which contain a capillary network, and a lymph vessel known as a lacteal. The cells covering the villi have a complex brush border composed of microvilli on their exposed membranes. These cells are replaced every 48 hours by the production of new cells as a result of mitosis at the base of the villi. The cells have many mitochondria in their cytoplasm close to the surface which lies next to the capillary network inside of the villus. Many of the soluble products of digestion diffuse into the cells through the brush borders and are then pumped by active transport into the capillaries to be taken away from the gut. Some substances are taken up only by diffusion.

The food is moved along the small intestine by peristalsis, the villi are also constantly in motion so that there surfaces are brought into contact with a constantly renewed source of absorbable materials.

Once the food leaves the small intestine and passes into the large intestine most of the useful products of digestion have been absorbed. The remaining fibrous material, roughage, forms a useful resource for the many micro-organisms living in the large intestines. These produce many vitamins and some amino acids which are absorbed into the bloodstream. Most of the water in the roughage will also be absorbed by the large intestine. Recent evidence shows that patches of specialised glandular material in the large intestine wall have the function of absorbing large molecules and organisms which are destroyed and checked for their antigen properties. It is believed that the prion proteins responsible for BSE in animals and CJD in humans is able to enter the body via these glands. Prion proteins are protease enzyme resistant and are not destroyed by their progress through the small intestines.

The faecal material enters the rectum which holds the material until sufficient has accumulated to stimulate egestion. The anal sphincters, one of smooth muscle controlled by the autonomic nervous system and another sphincter of striated muscle controlled by the conscious nervous systems will relax while a wave of peristalsis ejects the waste.