The gastrointestinal tract (digestive tract, digestional tract, GI tract, GIT, gut, or alimentary canal) is an organ system within humans and other animals which takes in food, digests it to extract and absorb energy and nutrients, and expels the remaining waste as feces. The mouth, esophagus, stomach and intestines are part of the gastrointestinal tract. Gastrointestinal is an adjective meaning of or pertaining to the stomach and intestines. A tract is a collection of related anatomic structures or a series of connected body organs.

All bilaterians have a gastrointestinal tract, also called a gut or an alimentary canal. This is a tube that transfers food to the organs of digestion.^[1] In large bilaterians, the gastrointestinal tract also has an exit, the anus, by which the animal disposes of feces (solid wastes). Some small bilaterians have no anus and dispose of solid wastes by other means (for example, through the mouth).^[1] The human gastrointestinal tract consists of the esophagus, stomach, and intestines, and is divided into the upper and lower gastrointestinal tracts.^[3] The GI tract includes all structures between the mouth and the anus,^[4] forming a continuous passageway that includes the main organs of digestion, namely, the stomach, small intestine, and large intestine. However, the complete human digestive system is made up of the gastrointestinal tract plus the accessory organs of digestion (the tongue, salivary glands, pancreas, liver and gallbladder).^[5] The tract may also be divided into foregut, midgut, and hindgut, reflecting the embryological origin of each segment. The whole human GI tract is about nine metres (30 feet) long at autopsy. It is considerably shorter in the living body because the intestines, which are tubes of smooth muscle tissue, maintain constant muscle tone in a halfway-tense state but can relax in spots to allow for local distention and peristalsis.^[6][7]

The gastrointestinal tract contains trillions of microbes, with some 4,000 different strains of bacteria having diverse roles in maintenance of immune health and metabolism.^[8][9][10] Cells of the GI tract release hormones to help regulate the digestive process. These digestive hormones, including gastrin, secretin, cholecystokinin, and ghrelin, are mediated through either intracrine or autocrine mechanisms, indicating that the cells releasing these hormones are conserved structures throughout evolution.^[11]

The structure and function can be described both as gross anatomy and as microscopic anatomy or histology. The tract itself is divided into upper and lower tracts, and the intestines small and large parts.^[12]

The upper gastrointestinal tract consists of the mouth, pharynx, esophagus, stomach, and duodenum.^[13] The exact demarcation between the upper and lower tracts is the suspensory muscle of the duodenum. This differentiates the embryonic borders between the foregut and midgut, and is also the division commonly used by clinicians to describe gastrointestinal bleeding as being of either "upper" or "lower" origin. Upon dissection, the duodenum may appear to be a unified organ, but it is divided into four segments based upon function, location, and internal anatomy. The four segments of the duodenum are as follows (starting at the stomach, and moving toward the jejunum): bulb, descending, horizontal, and ascending. The suspensory muscle attaches the superior border of the ascending duodenum to the diaphragm.

The suspensory muscle is an important anatomical landmark which shows the formal division between the duodenum and the jejunum, the first and second parts of the small intestine, respectively.^[14] This is a thin muscle which is derived from the embryonic mesoderm.

The lower gastrointestinal tract includes most of the small intestine and all of the large intestine.^[15] In human anatomy, the intestine (bowel, or gut. Greek: éntera) is the segment of the gastrointestinal tract extending from the pyloric sphincter of the stomach to the anus and, as in other mammals, consists of two segments, the small intestine and the large intestine. In humans, the small intestine is further subdivided into the duodenum, jejunum and ileum while the large intestine is subdivided into the, cecum, ascending, transverse, descending and sigmoid colon, rectum, and anal canal.^[16][17]

The small intestine begins at the duodenum and is a tubular structure, usually between 6 and 7 m long.^[18] Its mucosal area in an adult human is about 30 m2.^[19] Its main function is to absorb the products of digestion (including carbohydrates, proteins, lipids, and vitamins) into the bloodstream. There are three major divisions:

The large intestine also called the colon, consists of the cecum, rectum, and anal canal. It also includes the appendix, which is attached to the cecum. The colon is further divided into:

The main function of the large intestine is to absorb water.

The area of the large intestinal mucosa of an adult human is about 2 m2.^[19]

The gut is an endoderm-derived structure. At approximately the sixteenth day of human development, the embryo begins to fold ventrally (with the embryo's ventral surface becoming concave) in two directions: the sides of the embryo fold in on each other and the head and tail fold toward one another. The result is that a piece of the yolk sac, an endoderm-lined structure in contact with the ventral aspect of the embryo, begins to be pinched off to become the primitive gut. The yolk sac remains connected to the gut tube via the vitelline duct. Usually this structure regresses during development; in cases where it does not, it is known as Meckel's diverticulum.

During fetal life, the primitive gut is gradually patterned into three segments: foregut, midgut, and hindgut. Although these terms are often used in reference to segments of the primitive gut, they are also used regularly to describe regions of the definitive gut as well.

Each segment of the gut is further specified and gives rise to specific gut and gut-related structures in later development.

Components derived from the gut proper, including the stomach and colon, develop as swellings or dilatations in the cells of the primitive gut. In contrast, gut-related derivatives — that is, those structures that derive from the primitive gut but are not part of the gut proper, in general develop as out-pouchings of the primitive gut. The blood vessels supplying these structures remain constant throughout development.^[20]

The gastrointestinal tract has a form of general histology with some differences that reflect the specialization in functional anatomy.^[21] The GI tract can be divided into four concentric layers in the following order:

The mucosa is the innermost layer of the gastrointestinal tract.

The mucosa surrounds the lumen, or open space within the tube. This layer comes in direct contact with digested food (chyme). The mucosa is made up of:

The mucosae are highly specialized in each organ of the gastrointestinal tract to deal with the different conditions.

The most variation is seen in the epithelium.

The submucosa consists of a dense irregular layer of connective tissue with large blood vessels, lymphatics, and nerves branching into the mucosa and muscularis externa.

It contains the submucosal plexus, an enteric nervous plexus, situated on the inner surface of the muscularis externa.

The muscular layer consists of an inner circular layer and a longitudinal outer layer. The circular layer prevents food from traveling backward and the longitudinal layer shortens the tract. The layers are not truly longitudinal or circular, rather the layers of muscle are helical with different pitches. The inner circular is helical with a steep pitch and the outer longitudinal is helical with a much shallower pitch.^[22] Whilst the muscularis externa is similar throughout the entire gastrointestinal tract, an exception is the stomach which has an additional inner oblique muscular layer to aid with grinding and mixing of food. The muscularis externa of the stomach is composed of the inner oblique layer, middle circular layer and outer longitudinal layer.

Between the circular and longitudinal muscle layers is the myenteric plexus. This controls peristalsis. Activity is initiated by the pacemaker cells, (myenteric interstitial cells of Cajal). The gut has intrinsic peristaltic activity (basal electrical rhythm) due to its self-contained enteric nervous system. The rate can be modulated by the rest of the autonomic nervous system.^[22]

The coordinated contractions of these layers is called peristalsis and propels the food through the tract. Food in the GI tract is called a bolus (ball of food) from the mouth down to the stomach. After the stomach, the food is partially digested and semi-liquid, and is referred to as chyme. In the large intestine the remaining semi-solid substance is referred to as faeces.^[22]

The outermost layer of the gastrointestinal tract consists of several layers of connective tissue.

Intraperitoneal parts of the GI tract are covered with serosa. These include most of the stomach, first part of the duodenum, all of the small intestine, caecum and appendix, transverse colon, sigmoid colon and rectum. In these sections of the gut there is clear boundary between the gut and the surrounding tissue. These parts of the tract have a mesentery.

Retroperitoneal parts are covered with adventitia. They blend into the surrounding tissue and are fixed in position. For example, the retroperitoneal section of the duodenum usually passes through the transpyloric plane. These include the esophagus, pylorus of the stomach, distal duodenum, ascending colon, descending colon and anal canal. In addition, the oral cavity has adventitia.

Approximately 20,000 protein coding genes are expressed in human cells and 75% of these genes are expressed in at least one of the different parts of the digestive organ system.^[23][24] Over 600 of these genes are more specifically expressed in one or more parts of the GI tract and the corresponding proteins have functions related to digestion of food and uptake of nutrients. Examples of specific proteins with such functions are pepsinogen PGC and the lipase LIPF, expressed in chief cells, and gastric ATPase ATP4A and gastric intrinsic factor GIF, expressed in parietal cells of the stomach mucosa. Specific proteins expressed in the stomach and duodenum involved in defence include mucin proteins, such as mucin 6 and intelectin-1.^[25]

The time taken for food or other ingested objects to transit through the gastrointestinal tract varies depending on many factors, but roughly, it takes less than an hour after a meal for 50% of stomach contents to empty into the intestines while total emptying takes around 2 hours.

Subsequently, 50% emptying of the small intestine takes between 1 and 2 hours.

Finally, transit through the colon takes 12 to 50 hours with wide variation between individuals.^[26][27]

The gastrointestinal tract forms an important part of the immune system.^[28] The surface area of the digestive tract is estimated to be about 32 square meters, or about half a badminton court.^[29] With such a large exposure (more than three times larger than the exposed surface of the skin), these immune components function to prevent pathogens from entering the blood and lymph circulatory systems.^[30] Fundamental components of this protection are provided by the intestinal mucosal barrier which is composed of physical, biochemical, and immune elements elaborated by the intestinal mucosa.^[31] Microorganisms also are kept at bay by an extensive immune system comprising the gut-associated lymphoid tissue (GALT)

There are additional factors contributing to protection from pathogen invasion.

For example, low pH (ranging from 1 to 4) of the stomach is fatal for many microorganisms that enter it.^[32] Similarly, mucus (containing IgA antibodies) neutralizes many pathogenic microorganisms.^[33] Other factors in the GI tract contribution to immune function include enzymes secreted in the saliva and bile.

Beneficial bacteria also can contribute to the homeostasis of the gastrointestinal immune system.

For example, Clostridia, one of the most predominant bacterial groups in the GI tract, play an important role in influencing the dynamics of the gut's immune system.^[34] It has been demonstrated that the intake of a high fiber diet could be the responsible for the induction of T-regulatory cells (Tregs). This is due to the production of short-chain fatty acids during the fermentation of plant-derived nutrients such as butyrate and propionate. Basically, the butyrate induces the differentiation of Treg cells by enhancing histone H3 acetylation in the promoter and conserved non-coding sequence regions of the FOXP3 locus, thus regulating the T cells, resulting in the reduction of the inflammatory response and allergies.

The large intestine hosts several kinds of bacteria that can deal with molecules that the human body cannot otherwise break down.^[35] This is an example of symbiosis. These bacteria also account for the production of gases at host-pathogen interface, inside our intestine(this gas is released as flatulence when eliminated through the anus). However the large intestine is mainly concerned with the absorption of water from digested material (which is regulated by the hypothalamus) and the re absorption of sodium, as well as any nutrients that may have escaped primary digestion in the ileum.

Health-enhancing intestinal bacteria of the gut flora serve to prevent the overgrowth of potentially harmful bacteria in the gut. These two types of bacteria compete for space and "food," as there are limited resources within the intestinal tract. A ratio of 80-85% beneficial to 15–20% potentially harmful bacteria generally is considered normal within the intestines.

Enzymes such as CYP3A4, along with the antiporter activities, are also instrumental in the intestine's role of drug metabolism in the detoxification of antigens and xenobiotics.^[36]

There are many diseases and conditions that can affect the gastrointestinal system, including infections, inflammation and cancer.

Various pathogens, such as bacteria that cause foodborne illnesses, can induce gastroenteritis which results from inflammation of the stomach and small intestine. Antibiotics to treat such bacterial infections can decrease the microbiome diversity of the gastrointestinal tract, and further enable inflammatory mediators.^[37] Gastroenteritis is the most common disease of the GI tract.

Diverticular disease is a condition that is very common in older people in industrialized countries. It usually affects the large intestine but has been known to affect the small intestine as well. Diverticulosis occurs when pouches form on the intestinal wall. Once the pouches become inflamed it is known as diverticulitis.

Inflammatory bowel disease is an inflammatory condition affecting the bowel walls, and includes the subtypes Crohn's disease and ulcerative colitis. While Crohn's can affect the entire gastrointestinal tract, ulcerative colitis is limited to the large intestine. Crohn's disease is widely regarded as an autoimmune disease. Although ulcerative colitis is often treated as though it were an autoimmune disease, there is no consensus that it actually is such.

Functional gastrointestinal disorders the most common of which is irritable bowel syndrome. Functional constipation and chronic functional abdominal pain are other functional disorders of the intestine that have physiological causes, but do not have identifiable structural, chemical, or infectious pathologies.

Several symptoms are used to indicate problems with the gastrointestinal tract:

Gastrointestinal surgery can often be performed in the outpatient setting. In the United States in 2012, operations on the digestive system accounted for 3 of the 25 most common ambulatory surgery procedures and constituted 9.1 percent of all outpatient ambulatory surgeries.^[38]

Various methods of imaging the gastrointestinal tract include the upper and lower gastrointestinal series:

Intestines from animals other than humans are used in a number of ways.

From each species of livestock that is a source of milk, a corresponding rennet is obtained from the intestines of milk-fed calves. Pig and calf intestines are eaten, and pig intestines are used as sausage casings. Calf intestines supply calf-intestinal alkaline phosphatase (CIP), and are used to make goldbeater's skin. Other uses are:

Many birds and other animals have a specialised stomach in the digestive tract called a gizzard used for grinding up food.

Another feature not found in the human but found in a range of other animals is the crop. In birds this is found as a pouch alongside the esophagus.

Other animals including amphibians, birds, reptiles, and egg-laying mammals have a major difference in their GI tract in that it ends in a cloaca and not an anus.