Anatomy of the Gastrointestinal Tract

Gastrointestinal (GI) 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:

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.

Digestive System Diagram
Digestive System Diagram

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

Diagram of mouth, larynx and esophaguswhite spacer Diagram of mouth
Head and Neck and Isthmus of the Fauces

The Pharynx

Diagram of the Pharynx

The Esophagus

Esophageal Glands
Esophageal Glands

The Stomach

Diagram of the Stomach
Diagram of the Stomach

Lower GI Tract

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

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).

Diagram of Small Intestine
Small Intestine

The Duodenum

Duodenum-Brunner's Glands
Duodenum-Brunner's Glands

The Jejunum


The Ileum

Goblet Cells
Goblet Cells

Large Intestine

Diagram of Large Intestine
Large Intestine

The Cecum

Diagram of Cecum
Gray's Cecum

The Colon

Diagram of the Anorectum

Accessory Organs

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

The Liver

Diagram of the Liver

Diagram of the Biliary System
Biliary System

The Gallbladder

Diagram of the GallbladderWhite SpacerGallbladder haemalum-eosin stain
Gallbladder and Simple Columnar Epithelium

The Pancreas

Diagram of the 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 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 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 conduit for blood vessels, lymph vessels, and nerves serving the contained organs.

Stomach Layers DiagramWhite SpacerStomach Layers Diagram

Pediatric Diseases and Disorders of GI Anatomy

Diseases or disorders of the mouth and pharynx affected feeding 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 affecting 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 by the duodenum, jejunum and ileum) affecting 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 by the cecum, colon and rectum) affecting 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 affecting 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 affecting feeding can include: cholestasis, biliary colic, gallstones, cholecystitis, choledocholithiasis, cancer, and polyps (including primary sclerosing cholangitis)

Diseases or disorders of the pancreas affecting 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.

For further details related to GI Anatomy, also see the *Reflux and **Motility pages on this website.

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

Appendicitis / Appendectomy

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, and appendectomy (surgical removal of the appendix) can itself have long-term repercussions on the digestive process and feeding problems.

Symptoms of appendicitis can include:

Causes of appendicitis can include:

Acute Appendix
Acute Appendix

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 fifteen 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 ten 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 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 (EA)

Esophageal atresia 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 atresia, 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 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:

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

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 proper position.

Surgery may be required to straighten or remove the affected section. 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 (on motility page) and bowel atresia.

Symptoms of malrotation can include:

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. 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.

Return to Top

Links to key GI anatomy sites

National Digestive Diseases Information Clearinghouse (NDDIFC)

NNDIFC Easy-to-Read Publications

NNDIFC About Kids

International Foundation for Functional Gastrointestinal Disorders (IFFGD)

Pediatric Digital Library and Learning Collaboratory

General Citations

Bruce M. Carlson (2004). Human Embryology and Developmental Biology, 3rd edition, Saint Louis: Mosby

Complete Directory for Pediatric Disorders 2007/08 Edition, Grey House Publishing

Dorland's Illustrated Medical Dictionary, 31st Edition (2007)

Journal of Pediatric Gastroenterology & Nutrition. Lippincott Williams & Wilkins


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