Gastrointestinal physiology is the branch of human physiology that addresses the physical function of the gastrointestinal (GI) tract. The function of the GI tract is to process ingested food by mechanical and chemical means, extract nutrients and excrete waste products. The GI tract is composed of the alimentary canal, that runs from the mouth to the anus, as well as the associated glands, chemicals, hormones, and enzymes that assist in digestion. The major processes that occur in the GI tract are: motility, secretion, regulation, digestion and circulation. The proper function and coordination of these processes are vital for maintaining good health by providing for the effective digestion and uptake of nutrients.

The gastrointestinal tract generates motility using smooth muscle subunits linked by gap junctions. These subunits fire spontaneously in either a tonic or a phasic fashion. Tonic contractions are those contractions that are maintained from several minutes up to hours at a time. These occur in the sphincters of the tract, as well as in the anterior stomach. The other type of contractions, called phasic contractions, consist of brief periods of both relaxation and contraction, occurring in the posterior stomach and the small intestine, and are carried out by the muscularis externa.

Motility may be overactive (hypermotility), leading to diarrhea, or underactive (hypomotility), leading to constipation; either may cause abdominal pain or vomiting.

The stimulation for these contractions likely originates in modified smooth muscle cells called interstitial cells of Cajal. These cells cause spontaneous cycles of slow wave potentials that can cause action potentials in smooth muscle cells. They are associated with the contractile smooth muscle via gap junctions. These slow wave potentials must reach a threshold level for the action potential to occur, whereupon Ca²⁺ channels on the smooth muscle open and an action potential occurs. As the contraction is graded based upon how much Ca²⁺ enters the cell, the longer the duration of slow wave, the more action potentials occur. This, in turn, results in greater contraction force from the smooth muscle. Both amplitude and duration of the slow waves can be modified based upon the presence of neurotransmitters, hormones or other paracrine signaling. The number of slow wave potentials per minute varies based upon the location in the digestive tract. This number ranges from 3 waves/min in the stomach to 12 waves/min in the intestines.

The peristalsis and segmentation, detailed below and pendular movement are famous examples of distinct patterns of GI contraction. Occurring between meals, the migrating motor complex is a series of peristaltic wave cycles in distinct phases starting with relaxation, followed by an increasing level of activity to a peak level of peristaltic activity lasting for 5–15 minutes. This cycle repeats every 1.5–2 hours but is interrupted by food ingestion. The role of this process is likely to clean excess bacteria and food from the digestive system.

Peristalsis is one of the patterns that occur during and shortly after a meal. The contractions occur in wave patterns traveling down short lengths of the GI tract from one section to the next. The contractions occur directly behind the bolus of food that is in the system, forcing it toward the anus into the next relaxed section of smooth muscle. This relaxed section then contracts, generating smooth forward movement of the bolus at between 2–25 cm per second. This contraction pattern depends upon hormones, paracrine signals, and the autonomic nervous system for proper regulation.

Segmentation contractions also occur during and shortly after a meal within short lengths in segmented or random patterns along the intestine. This process is carried out by the longitudinal muscles relaxing while circular muscles contract at alternating sections thereby mixing the food. This mixing allows food and digestive enzymes to maintain a uniform composition, as well as to ensure contact with the epithelium for proper absorption.

Every day, seven liters of fluid are secreted by the digestive system. This fluid is composed of four primary components: ions, digestive enzymes, mucus, and bile. About half of these fluids are secreted by the salivary glands, pancreas, and liver, which compose the accessory digestive organs of the digestive system. The rest of the fluid is secreted by the GI epithelial cells.