GI Anatomy and Disease

Anatomy of the Gastrointestinal Tract

Organs digestive system

Digestive System Diagram

Gastrointestinal Tract

The gastrointestinal (GI) tract (also digestive tract, or alimentary canal) is the system of organs in the body that takes in food, digests it for the absorption of nutrients and energy, and expels waste material. The major functions of the GI tract are categorized as four distinct processes:

Ingestion is the consumption of food and other substances through the mouth, as they pass by chewing and swallowing into the GI tract.

Digestion is the process of metabolism by which ingested substances are mechanically and chemically converted for use by the body. Digestion is further categorized into three distinct phases: the cephalic phase in which taste and smell stimulate the nervous system to prepare the body for eating and digestion; the gastric phase in which passage of food into the stomach stimulates the release of gastric juices and pH balancing mechanisms throughout the system; and the intestinal phase in which excitatory and inhibitory reflexes control the passage of partially digested food into and through the intestines.

Absorption is the movement of metabolized nutrients and water from the digestive system into the circulatory and lymphatic capillaries by osmosis, active transport, and diffusion through the cells in the walls and surrounding layers of intestines and their supporting circulatory systems.

Excretion or egestion is the elimination of undigested, mostly solid material from the GI tract by defecation. Fluid products of metabolism throughout the body are also excreted by organ systems not directly part of the GI tract and digestive system, such as the kidneys, skin, and lungs.

In addition to processing nutrients as the principal pathways of the digestive system, the GI tract is also a prominent part of the immune system, providing various levels of defense against pathogenic microorganisms and potentially toxic substances throughout the path of digestion. Dysfunction anywhere in the GI tract, whether by disease, trauma, or anatomical anomaly, can result in symptoms or conditions affecting the well-being of the entire individual. Many diseases and disorders of the GI tract can result in feeding difficulties in children and infants.

The GI tract is conventionally divided into upper and lower parts, with associated accessory organs.

Upper GI Tract

The upper GI tract consists of the mouth, pharynx, esophagus, and stomach. This is where ingestion and the first phase of digestion occur.

The Mouth

oral cavity

Head and Neck and Isthmus of the Fauces
  • Includes the tongue, teeth, and buccal mucosa or mucous membranes containing the ends of the salivary glands, continuous with the soft palate, floor of the mouth, and underside of the tongue.
  • Chewing (mastication) is the mechanical process by which food, constantly repositioned by the muscular action of the tongue and cheeks, is crushed and ground by the teeth through the muscular action of the lower jaw (mandible) against the fixed resistance of the upper jaw (maxilla).
  • Saliva excreted in the oral cavity by three pairs of exocrine glands (parotid, submandibular, and sublingual) is mixed with chewed food to form a bolus, or ball-shaped mass.
  • There are two types of saliva: a thin watery secretion that wets the food and a thick mucus secretion that lubricates and causes the food particles to stick together to form the bolus.
  • Digestive enzymes in saliva begin the chemical breakdown of food, primarily starches at this point, almost immediately.

The Pharynx

  • The pharynx is contained in the neck and throat, and functions as part of both the digestive system and the respiratory system.
  • The human pharynx is divided into three sections:
    1. The nasopharynx behind the nasal cavity and above the soft palate.
    2. The oropharynx behind the oral cavity and including the base of the tongue, the tonsils, and the uvula.
    3. The hypopharynx or laryngopharynx includes the junction with the esophagus and the larynx, where respiratory and digestive pathways diverge.
  • The swallowing reflex is initiated by touch receptors in the pharynx as the bolus of chewed food is pushed to the back of the mouth.
  • Swallowing automatically closes down the respiratory or breathing pathway as an anti-choking reflex.
  • Failure or confusion of reflexes at this point can result in aspiration of solid or liquid food into the trachea and lungs.

The Esophagus

Esophageal Glands
  • The esophagus is the hollow muscular tube through which food passes from the pharynx to the stomach.
  • It is lined with a mucous membrane, which is continuous with the mucosa of the mouth, and into which the esophageal glands open.
  • It is surrounded by relatively deep muscles that move the swallowed bolus of masticated food through peristaltic action, piercing the thoracic diaphragm to reach the stomach.

The Stomach

Diagram of the Stomach
  • The stomach is a hollow muscular organ, located below the diaphragm and above the small intestine, which receives and holds masticated food to begin the next phase of digestion.
  • Two smooth muscle valves, the esophageal sphincter above and the pyloric sphincter below, keep stomach contents contained.
  • The stomach is surrounded by stimulant (parasympathetic) and inhibitor (orthosympathetic) nerve plexuses, which regulate both secretory and muscular activity during digestion.
  • With a volume of as little as 50 mL when empty, the adult human stomach may comfortably contain about a liter of food after a meal, or uncomfortably as much as 4 liters of liquid.

Lower GI Tract

The lower GI tract includes the small intestine and large intestine, beginning after the stomach and terminating at the anus. Its function is to complete the digestion and absorption of nutrients and to prepare waste products for elimination from the digestive system.

Small Intestine

Small Intestine

The small intestine is where most digestion takes place. It is structurally divided into three parts: the duodenum, the jejunum, and the ileum. Among humans over five years old, the small intestine tends to vary in length from 4–7 meters (13–23 feet).

Duodenum-Brunner’s Glands

The Duodenum

  • The duodenum consists of four parts, with the first three forming a “C” shape.
    1. The first or superior part of the duodenum begins at the pylors, passing laterally for a short distance before curving into the superior duodenal flexure.
    2. The second, or descending, part of the duodenum passes from the superior into the inferior duodenal flexure, and is where the pancreatic and common bile ducts enter the GI tract.
    3. The third or inferior horizontal part of the duodenum passes from the inferior flexure, crossing the aorta (major artery) and inferior vena cava (major vein), as well as the spinal column.
    4. The forth or ascending part of the duodenum passes over the aorta, and curves past the pancreas to the duodenojejunal flexure.
    5. The duodenum is where most of the breakdown of food in the small intestines occurs.
    6. It is here that Brunner’s glands produce an alkaline secretion to protect the duodenum from acidic chyme entering from the stomach, and to activate intestinal enzymes enabling digestion and absorption.

The Jejunum

  • The jejunum begins at the ligament of Treitz in the duodenojejunal flexure, and continues to the ileum.
  • The inner surface or mucous membrane of the jejunum is covered by villi (small, finger-like structures) much longer than found in the duodenum or ileum, contained in many large circular folds (plicae circulares), which provide extensive surface area for absorption of nutrients.
    1. The villi can increase intestinal absorptive surface area by a factor of 30.
    2. The microvilli, extensions of the villi, increase the surface area by an additional factor of 600.
    3. Villus capillaries collect amino acids and simple sugars.
    4. Villus lacteals or lymphatic capillaries absorb dietary fats.

The Ileum

Goblet Cells
  • The ileum is the final and longest section of the small intestine.
  • Both the jejunum and the ileum are suspended by mesentery, a double layer of peritoneum that allows these parts of the intestine to move more freely within the abdomen.
  • Like the jejunum, the wall of the ileum has many folds and villi to increase both the absorption of enzymes and absorption of nutrients. It also has an increasing number of goblet cells.
  • The ileum is responsible for the final stages of protein and carbohydrate digestion, as contents are pushed along by peristaltic waves of smooth muscle contractions.
  • There is no absolute demarcation between the jejunum and the ileum, but the ileum tends to have more fat inside the mesentery and has a relatively decreasing diameter.
  • Unlike the rest of the small intestine, the ileum has abundant Peyer’s patches, lymphoid follicles similar to lymph nodes, which function as an important component of the immune system response to pathogenic organisms in the GI tract.

Large Intestine

Large Intestine
  • Also commonly referred to by the name of its longest component, the colon, the large intestine is the last part of the digestive system.
  • Its principal function is to absorb remaining water from the waste products of digestion as it compacts the accumulated waste for periodic elimination by defecation.
  • While food is not broken down further at this stage, the fluid absorption function of the large intestine does act to gather in vitamins created by beneficial bacteria or flora inhabiting the colon.
  • Instead of the predominance of evaginations of villi found in the small intestine, the large intestine has increased invaginations of glands and an abundance of goblet cells. The large intestine is structurally divided into three parts: the cecum, colon, and rectum.

The Cecum

Gray’s Cecum
  • The cecum is a pouch at the beginning of the large intestine, separated from the ileum of the small intestine by the ileocecal lower right quadrant of the abdomen.
  • The cecum is host to a large number of bacteria, which aid in the final enzymatic processing of material not completely digested in the small intestine.
  • The vermiform appendix is a worm-like cul-de-sac attachment of the cecum, until recently considered entirely vestigial in humans, but now thought to have a role as a haven for the beneficial gut flora, as well as the site of infection-fighting lymphoid cells.

The Colon

    • The colon consists of four parts named for their relative orientation in the abdomen and the rectum:
  1. The ascending colon (1)
  2. The transverse colon (2)
  3. The descending colon (3)
  4. The sigmoid colon (4)
  5. The rectum (5)

  • By the time the chyme has reached the colon, almost all nutrients and most of the water have already been absorbed by the body.
  • It is here that the chyme is mixed with mucus and bacteria to become feces. The waste products of bacterial metabolism include some nutrients used by the cells lining the colon for their own nourishment.
  • The colon ends at the junction of the sigmoid colon and the rectum.
    1. The rectum is the last part of the large intestine, beginning at and continuous with the colon, and terminating at the anus.
    2. The rectum provides a temporary storage for feces.
    3. Stretch receptors of the nervous system located in the rectal walls stimulate the desire to defecate. As peristaltic waves propel the feces into the anal canal, external and internal sphincters allow the final exit of waste material from the GI tract.

Accessory Organs

Accessory to the alimentary canal of the GI tract are various secretory, storage, and waste filtering organs, as well as and related hormonal glands. Principal among these are the liver, gallbladder, and pancreas.

The Liver


Biliary System
  • The liver secretes bile, produced by its hepatocytes, into the duodenum of the small intestine via the biliary system. Bile acts as a kind of detergent, emulsifying fats to promote enzyme action in the intestines.
  • Epithelial cells in the liver add a watery solution, rich in bicarbonates, which acts to dilute and neutralize acids at this stage of digestion.
  • Cholesterol is also released with the bile and is important for the metabolism of fat soluble vitamins, as well as the maintenance of normal cell membranes throughout the body.
  • Consistent with its major role in metabolism, the liver has a number of functions not strictly related to digestion, such as the decomposition of red blood cells, plasma protein synthesis, and detoxification.
  • The liver is the largest gland in the human body and performs or regulates a wide variety of high-volume reactions involving very specialized tissues.

The Gallbladder

Gallbladder and Simple Columnar Epithelium
  • The gallbladder is connected to the liver and the duodenum by the biliary tract.
  • The gallbladder stores the bile (or gall) secreted by the liver until its release is triggered by the digestive process.
  • The interior of the gallbladder has a simple columnar epithelial lining characterized by recesses or pouches, which provide the volume for storage.
  • The cystic duct connects the gallbladder to the common hepatic duct to form the common bile duct.

The Pancreas

  • The pancreas is another relatively large gland that functions as part of both the digestive and endocrine system.
  • Its exocrine function is to produce and secrete pancreatic juice rich in digestive enzymes.
  • Its endocrine functions include the production of important hormones such as:
    1. Insulin, which helps regulate metabolism at the global and cellular level
    2. Glucagon, which acts opposite insulin
    3. Somatostatin, which acts to suppress the release of various other GI hormones and lower the rate of gastric emptying as digestion approaches completion
  • The pancreatic duct joins the common bile duct, together entering the major duodenal papilla through the hepatopancreatic ampulla.
  • Because the human pancreas is not completely matured until age two, otherwise normal infants will have digestive problems with entire categories of foods until all the appropriate enzymes can be properly secreted by the fully developed pancreas.

GI Histology

In addition to the sequential phases of digestion, and the corresponding structure and function of each specific organ in the digestive system, the GI tract is characterized as having four concentric layers of tissue with functional differences in each specialized region.

The Mucosa



  • The mucosa (moist linings of mucous membranes) is the first main layer, and consists of:
    1. The primary epithelium, tissues lining the cavities, and surfaces of structures throughout the body
    2. The lamina propria, containing capillaries, lymph vessels, and glands with ducts opening on to the epithelium
    3. The muscularis mucosae, a thin layer of smooth muscle

The Submucosa

The submucosa consists of fibrous connective tissue, separating the mucosa from the surrounding muscles, and includes fine bundles of nerve plexuses.

The Muscularis Externa

  • The muscularis externa, external muscle layer, generally has two distinct layers of smooth muscle: the inner (circular) and outer (longitudinal).
  • In the stomach, there is a third layer (inner oblique) responsible for the churning or mechanical breakdown of food.
  • In the esophagus, part of the external muscle layer is skeletal muscle rather than smooth muscle.
  • The pyloric and anal sphincters are also formed by the inner layer of the muscularis externa.

The Serosa

The serosa (serous membrane) consists of layers of connective tissue continuous with the peritoneum, which forms the lining of the abdominal cavity and serves as a conduit for blood vessels, lymph vessels, and nerves serving the contained organs.

Pediatric Diseases and Disorders of GI Anatomy

Diseases or disorders of the mouth and pharynx affect feeding and can include strep throat, tonsillitis, mumps, chronic sore throat, cleft palate, or the more general velocardiofacial syndrome (VCFS), temporomandibular (TMD), and the entire spectrum of dental disease and disorders.

Diseases or disorders of the esophagus that affect feeding can include peptic strictures, atresia with or without tracheoesophageal fistula, achlasia, ingestion or aspiration of foreign or caustic material, and gastrointestinal reflux disease (GERD).

Diseases or disorders of the stomach affecting feeding can include: dyspepsia, stomach ache, chronic vomiting syndrome (CVS), peptic gastric ulcer, achlrohydria, hypochlorhydria, hyperchlorhydria, linitis plastica or Brinton’s disease (a form of stomach cancer), Zollinger-Ellison syndrome (extremely rare in children), gastroparesis, gastroenteritis, borborygmus, and GERD.

Diseases or disorders of the small intestine (comprised of the duodenum, jejunum, and ileum) that affect feeding can include peptic ulcer, atresia, alimentary hypoglycemia, celiac disease, rapid gastric emptying (dumping syndrome, early and late), connective tissue conditions such as Ehlers-Danlos syndrome, various infectious diseases (such as giardiasis, scariasis, tropical sprue, or tapeworm), gastroenteritis, and other imbalances of intestinal flora.

Diseases or disorders of the large intestine (comprised of the cecum, colon, and rectum) that affect feeding can include: appendicitis, atresia, colitis, colon cancer, Hirschsprung’s disease, inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), malrotation, and various other syndromes and conditions manifesting as either constipation or diarrhea.

Disease or disorders of the liver that affect feeding can include: hepatitis, hemochromatosis, cancer, primary sclerosing cholangitis, Gilbert’s syndrome, and Wilson’s disease. There are many primarily pediatric liver diseases, including but by no means limited to: biliary atresia, antitrypsin deficiency, alagille syndrome, neonatal jaundice, and progressive intrahepatic cholestasis. A number of liver function tests are available to evaluate the proper functioning of the liver by isolating the presence of certain enzymes in the blood.

Diseases or disorders of the gallbladder that affect feeding can include: cholestasis, biliary colic, gallstones, cholecystitis, choledocholithiasis, cancer, and polyps (including primary sclerosing cholangitis).

Diseases or disorders of the pancreas that feeding can include: diabetes mellitus, benign tumors, cystic fibrosis, exocrine pancreatic insufficiency, hemosuccus pancreaticus, acute and chronic pancreatitis, and Zollinger-Ellison syndrome (extremely rare in children). Since the pancreas is not fully developed until age two, temporary deficiencies of digestive enzymes must be considered normal in infants.

Diagnostic Tools



Several tools are available to the physician or specialist for identifying, evaluating, and diagnosing disorders, malformations, and obstructions throughout the anatomy of the GI tracts in infants, children, and adults. Most common among these are biopsy, barium swallow, pH probe, x-ray, CT scan and upper or lower endoscopy.

A Closer Look



Acute Appendix

Appendicitis is an acute condition characterized by inflammation of the vermiform appendix, and is recognized as one of the most common causes of abdominal pain in humans worldwide. In addition to the immediate symptoms and effects of acute appendicitis, an appendectomy (surgical removal of the appendix) can itself have long-term repercussions on the digestive process and feeding problems.appendectomy

Symptoms of appendicitis can include:

  • Typical: Initially centralized pain localizing the lower right side of the abdomen (right iliac fossa), accompanied by loss of appetite and fever, with or without nausea and vomiting.
  • Atypical: Pain beginning and staying in the right iliac fossa, diarrhea, or involvement of the bladder resulting in frequent micturition or urination.

Causes of appendicitis can include:

  • Fecalith, fecaloma (i.e. tumor made of feces), and coprolith (i.e. stones made of feces) are different names for chronic obstructions of the colon by hardening of the feces. Fecal impaction itself has a variety of possible causes and other effects, which must be considered in a diagnosis of appendicitis, but a fecalith is usually the cause of acute appendicitis.
  • Other primary obstructions of the appendix lumen by foreign bodies, trauma, intestinal worms, or lymphadenitis.
  • Low dietary fiber intake and the resulting increased transit time of fecal matter have been implicated in the pathogenesis of appendicitis.

Peritonitis is an inflammation of the serous membrane lining the abdominal cavity and some of the organs contained within. It may be acute or generalized, but generally depends on an infection spread by the rupture of an internal organ, most commonly an appendix. The real danger of this life-threatening condition is why acute appendicitis warrants immediate evaluation and treatment. In children, particularly, differential diagnosis must also consider gastroenteritis, mesenteric adenitis, Meckel’s diverticulitis, intussusceptions, Henoch-Schonlein purpura, and lobar pneumonia.

Treatment begins by cessation of all eating or drinking, even water, for a period before surgery. An intravenous drip may be used to keep the patient hydrated. Antibiotics may also be administered intravenously to inhibit the spread of infection and other postoperative complications. Surgical removal of the appendix can be accomplished laparoscopically in simple cases, but may be converted to open laparotomy if necessary due to rupture, abscess, or adhesions. It may last from 15 minutes in typical appendicitis in thin or small patients to several hours in complicated cases. Hospital stays range from overnight to a matter of days, sometimes weeks in rare cases. The pain is not always constant, sometimes stopping for a day and then returning.

Most appendicitis patients recover easily, but complications can ensue if treatment is delayed or peritonitis has occurred, usually due to a rupture of the infected organ before treatment. For young children up to 10 years old, complete recovery takes about three weeks, with minor dietary restrictions. Constipation can be a problem for a few days following surgery and bowel movements should be monitored.

Long-term effects of the loss of an appendix are not considered critical, and there is no reasonable chance to save the infected organ. A healthy appendix is now thought to have a key role in the recovery of intestinal flora from flushing out caused by diarrhea, so it is not unreasonable to assume that the absence of an appendix may impact or delay recovery under similar circumstances.


Atresia is a condition in which an orifice or passage in the body in abnormally closed or absent. It may occur at any of several points along the GI tract, and each are considered a congenital malformation or birth defect. Some atresias can be detected before birth during routine sonograms.

Esophageal Atresia

Esophageal atresia (EA) is a failure of the esophagus to develop as a continuous passage, ending instead in a blind pouch. It may occur together with or separately from tracheoesophageal fistula (TEF), an abnormal opening between the trachea and the esophagus. EA is suspected in newborn infants with excessive drooling, choking, coughing, and sneezing. Respiratory distress is typical.

If a catheter finds resistance or complete blockage, then other tests or scans can confirm the diagnosis. Oral feeding is stopped and intravenous fluids are started. Surgery will usually repair the defect and complete recovery and normal development are typical with appropriate post-surgical care and feeding, but babies with EA may have other congenital problems, sometimes involving the heart, spine, or kidneys, which will require diagnosis and treatment during infancy.

Biliary Atresia

Biliary atresia is a rare condition in newborn infants, in which the common bile duct is blocked or absent. If unrecognized or untreated, it leads to liver failure. Its symptoms are initially indistinguishable from neonatal jaundice (a more common condition). If the intrahepatic biliary tree is unaffected, surgery can reconstruct the defect (Kasai procedure). If the atresia is complete, a liver transplant is necessary.

Intestinal Atresia

Intestinal atresia, including duodenal, jejunal, ileal, and colon atresia, may show up in sonograms as dilated intestinal segments due to the blockage, or by the buildup of too much amniotic fluid in the mother’s uterus. Some fetal bowel obstructions are chromosomal in origin, and amniocentesis may reveal these abnormalities. Fetal and neonatal intestinal atresia are corrected surgically after birth, either completely or by temporary use of a stoma.

Anal Atresia

Anal atresia, or imperforate anus, is a congenital defect in which the rectum is malformed or completely closed at the anus. There are several forms, and as with most atresias, they are usually present with other problems involving the heart, spine, or kidneys.

Surgical correction with or without protective colostomy is usually taken within the first day of life. Depending on the location of the lesion, children with a corrected imperforate anus may or may not have problems with bowel control, but will almost always have problems with constipation. Further surgery later in life may adjust the angle between the anus and rectum, and/or remove an excessively dilated section of colon, improving outcomes for both continence and constipation.


Sometimes one section of the bowel tunnels into an adjoining section, much like a collapsible telescope. Called intussusception, this condition can occur in either the small intestine or the large intestine, or between them. In infants and children, intussusception is one of the most common causes of intestinal obstruction.

Symptoms of intussusception can include:

  • Bowel movements mixed with blood and mucus
  • Dehydration
  • Diarrhea
  • Distention or lump in the abdomen
  • Fever
  • Intermittent abdominal pain
  • Lethargy
  • Vomiting bile
  • Shock (e.g. low blood pressure, elevated pulse) requiring immediate attention.

Causes of intussusception in children are not fully understood, but may include:

  • Viral infection
  • Vaccine for rotavirus (no longer given)
  • Malrotation

If intussusception is not diagnosed promptly, it can cause serious damage to the affected portion of the lower GI tract. A range of diagnostic tests can be applied to identify the condition and possibly identify an underlying cause. X-rays of the abdomen may suggest a bowel obstruction. Upper and lower GI series can locate the telescoping. CT scans may help. An air or barium enema may sometimes correct the problem, if not the original cause, by pushing the affected section of the bowel into the proper position.

Surgery may be required to straighten or remove the affected section. The outcome depends on the stage of intussusception at diagnosis and the underlying cause, but with early treatment, the prognosis is generally excellent. In some cases, intussusception in children may be temporary and resolve spontaneously.

Malrotation and Volvulus

Sometimes during embryonic development, a section of the lower GI tract may not rotate completely into its final position. This condition is called malrotation. If the cecum of the large intestine is not positioned correctly, the bands of tissue that normally hold it in place may cross over and block part of the small intestine. If either the small or large intestines have not rotated completely, the supporting mesentery may be incompletely attached to the back of the abdominal cavity, resulting in a mobile or floppy bowel prone to twisting, a condition called volvulus (either cecal and sigmoid, which is more common). Malrotation is associated with other GI conditions, such as Hirschsprung’s disease and bowel atresia.

Symptoms of malrotation can include:

  • Vomiting bile (especially in infants)
  • Abdominal pain
  • Diarrhea
  • Constipation
  • Bloody stool or rectal bleeding
  • Failure to thrive

Causes of malrotation are unclear, but it is considered a congenital abnormality. Most cases are identified in infants, and most of those in the first month of life.

Diagnosis and testing include x-rays to determine if there is a blockage, upper GI series to locate the point of obstruction, and lower GI series to determine the position of the colon. A CT scan may also be used.

Surgery to relieve blockage caused by malrotation is generally successful and allows the digestive system to function and develop normally.

Links to Key GI Anatomy Sites

General Citations

  1. Bruce M. Carlson (2004). Human Embryology and Developmental Biology, 3rd edition, Saint Louis: Mosby.
  2. Complete Directory for Pediatric Disorders 2007/08 Edition, Grey House Publishing.
  3. Dorland’s Illustrated Medical Dictionary, 31st Edition (2007).
  4. Journal of Pediatric Gastroenterology & Nutrition. Lippincott Williams & Wilkins.