Upper GI Tract Anatomy

Updated: Jun 28, 2016
  • Author: Vinay K Kapoor, MBBS, MS, FRCSEd, FICS, FAMS; Chief Editor: Thomas R Gest, PhD  more...
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The GI, or digestive, tract extends from mouth to anus (see the image below). The division of the GI tract into upper and lower is a matter of some confusion and debate. On embryologic grounds, the GI tract should be divided into upper (mouth to major papilla in the duodenum), middle (duodenal papilla to mid-transverse colon), and lower (mid-transverse colon to anus), according to the derivation of these 3 areas from the foregut, midgut, and hindgut, respectively.

Digestive tract, anterior view. Digestive tract, anterior view.

Nevertheless, the GI tract is conventionally divided into upper (mouth to ileum) and lower (cecum to anus). From the point of view of GI bleeding, however, the demarcation between the upper and lower GI tract is the duodenojejunal (DJ) junction (ligament of Treitz); bleeding above the DJ junction is called upper GI bleeding, and that below the DJ junction is called lower GI bleeding.


Gross Anatomy

Mouth, oral cavity, and pharynx

The mouth (the opening between the upper and lower lips) leads to the oral cavity, which has a vestibule lying between the lips, the cheeks and gums (gingivae), and the teeth. The main oral cavity lies between the hard and soft palate above, the tongue below, and the alveoli and teeth. Salivary gland ducts (parotid, submandibular, and sublingual) open into the oral cavity. The oral cavity leads to the pharynx through the fauces, which contain pharyngeal tonsils (adenoids) and palatine tonsils. 

The pharynx extends from the base of the skull above to the cricoid cartilage (at the level of C6) below. It has 3 parts: the nasopharynx (from the base of the skull above to the soft palate below), the oropharynx (from the soft palate above to the hyoid bone below), and the laryngopharynx (from the hyoid bone above to the cricoid cartilage below). The nasal cavity, oral cavity, and larynx open into the nasopharynx, oropharynx, and laryngopharynx, respectively. The laryngopharynx also has a piriform fossa on either side.


The esophagus (gullet) is one of the few organs traversing 3 regions of the body: the neck, thorax, and abdomen. Accordingly, it is divided into 3 parts: cervical, thoracic, and abdominal. The esophagus is a 25-cm-long (other 25-cm-long organs are the duodenum and the ureter) vertical muscular tube that normally remains collapsed and that runs from the laryngopharynx (throat or hypopharynx) in the neck through the thorax (chest) to the stomach in the abdomen.

The cervical esophagus begins at the lower border of the cricoid cartilage (at the level of C6); it is very short (only 5 cm long) and lies in front of C6 and C7 (covered with prevertebral fascia), slightly to the left of the midline. In the neck, the esophagus, along with the trachea (in front of the esophagus) and the thyroid (covering the trachea and the esophagus), is enclosed in a sheath of visceral (deep cervical) fascia.

The carotid sheath (containing the common carotid artery, internal jugular vein, and vagus nerve) is on the side of the esophagus; the recurrent laryngeal nerves lie in the tracheoesophageal grooves, and the thoracic duct is to the left of the esophagus.

The cervical esophagus continues as the thoracic esophagus at the suprasternal notch. In the superior mediastinum, the esophagus continues to run in front of the vertebral column and behind the trachea and lies behind the aortic arch and to the right of the descending thoracic aorta. The azygos vein crosses in front of the esophagus on the right.

In the posterior mediastinum, the esophagus continues behind the left main bronchus and right pulmonary artery and comes to lie in front of the descending thoracic aorta at the esophageal hiatus of the diaphragm. The thoracic duct lies to the left of the esophagus in the superior mediastinum and behind it in the posterior mediastinum. Mediastinal pleurae lie laterally, and the pericardial sac lies anterior to the esophagus.

The thoracic esophagus enters the abdomen via the esophageal hiatus in the diaphragm at the level of T10 (see the image below) and has a small (2-3 cm) intra-abdominal length. The esophagogastric junction (cardia), therefore, lies in the abdomen below the diaphragm to the left of the midline at the level of T11.

Upper GI tract, coronal section. Upper GI tract, coronal section.


The cardiac notch (incisura cardiaca gastri) is the acute angle between the left border of the intra-abdominal esophagus and the gastric fundus (the part of the stomach above a horizontal line drawn from the cardia). The fundus of the stomach is related to the undersurface of the left dome of diaphragm and spleen. The body (corpus) of the stomach leads to the pyloric antrum (at the incisura angularis), which joins the duodenum at the pylorus, lying at the L1-L2 level (transpyloric plane) to the right of the midline. The stomach has a shorter concave lesser (right) curvature and a longer convex greater (left) curvature. The lesser curvature is attached to the undersurface of the liver by lesser (gastrohepatic) omentum and the greater curvature is attached to the transverse colon by greater (gastrocolic) omentum.  


The duodenum has 4 parts: superior, descending, horizontal, and ascending.

The first (superior) part, or bulb (5 cm), is connected to the undersurface of the liver (porta hepatis) by the hepatoduodenal ligament (HDL), which contains the proper hepatic artery, portal vein, and common bile duct (CBD); the quadrate lobe of the liver and gallbladder are in front, and the CBD), portal vein, and gastroduodenal artery (GDA) are behind.

The second (descending) part, or C loop (10 cm), which has an upper and a lower genu (flexure), is composed of the transverse mesocolon and colon in front and the right kidney and inferior vena cava (IVC) behind; the head of the pancreas lies in the concavity of the C.

The third (horizontal) part (7.5 cm) runs from right to left in front of the inferior vena cava (IVC) and aorta, with superior mesenteric vessels (the vein on the right and the artery on the left) in front.

The fourth (ascending) part (2.5 cm) continues as the jejunum. The duodenum continues into the jejunum at the duodenojejunal flexure.

The rest of the small bowel (jejunum and ileum) is a convoluted tube about 4-6 m long that occupies the center of the abdomen and the pelvis, surrounded on 2 sides and above by the colon. The ileum continues into the large intestine at the ileocecal junction.

Anatomy on diagnostic imaging

The pharynx and esophagus are evaluated by barium swallow; areas of normal constriction in the esophagus are the pharyngoesophageal junction (at the level of C6), the aortic arch (at the level of T2-T3), the left bronchus (at the level of T4-T5), and the esophageal hiatus in the diaphragm (at the level of T10). Barium meal helps to evaluate the stomach and duodenum. A small bowel follow-through helps to evaluate the small intestine (jejunum and ileum). Enteroclysis involves injection of radiological contrast directly into the proximal jejunum through a nasojejunal tube - it provides better delineation of small intestine. Computed tomography can also be combined with enteroclysis. 

A rigid pharyngoscope visualizes various parts of the pharynx. The esophagus (along with the stomach and duodenum) is evaluated by esophagogastroduodenoscopy (EGD), also called upper GI endoscopy, which is performed with a flexible fiberoptic endoscope with the patient under sedation. Endoscopic landmarks include the cricopharyngeus (15 cm from the upper incisors), the aortic arch (22 cm), the left bronchus (27 cm), and the Z line (the transition from pale-pink esophageal to bright-pink gastric mucosa), and the cardia (40 cm). 

For the purposes of endoscopy, the upper GI tract includes the esophagusstomach and duodenum (esophagogastroduodenoscopy [EGD] or upper GI endoscopy UGIE), and the lower GI tract includes the anus, rectum, colon, and cecum (anoproctosigmoidocolonoscopy or lower GI endoscopy). [1, 2, 3]  The small intestine (jejunum and ileum) is relatively inaccessible to endoscopy. The proximal jejunum can be examined by push enteroscopy using balloon tipped upper GI endoscopes whereas the distal ileum can be examined by retrograde ileoscopy at colonoscopy. Capsule endoscopy can examine the entire small intestine.


Microscopic Anatomy

The upper GI tract has the usual 4-layer structure characteristic of the rest of the GI tract.

The innermost mucosa contains mucous membrane, lamina propria, and muscularis mucosa. The submucosa contains a rich vascular network. The muscular layer includes inner circular and outer longitudinal muscles. The outer surface is covered with serosa.

Wall layers on ultrasonography

Endoscopic ultrasonography (EUS) is the latest technical tool for evaluating the esophagus. An ultrasound probe is mounted at the tip of an upper GI endoscope, which is passed into the esophagus. The wall of the esophagus is seen as 5 alternating layers, as follows:

  1. Mucosa (hyperechoic)

  2. Lamina propria (hypoechoic)

  3. Submucosa (hyperechoic)

  4. Muscularis propria (hypoechoic)

  5. Adventitia (hyperechoic)

EUS is very helpful in the diagnosis and staging of early esophageal and gastric cancer. It can be used to visualize periesophageal and perigastric lymph nodes and to guide fine-needle aspiration cytology from them.


Pathophysiologic Variants

Duplication cysts can occur in any part of the GI tract.

Atresia can involve esophagus, duodenum and small intestine (jejunum and ileum).

Esophageal atresia results from failure of recanalization of the foregut. In the most common variant, the proximal stump of the esophagus ends blindly, and the distal stump of the esophagus is connected to the trachea (tracheoesophageal fistula).

Zenker’s false diverticulum (so called because it contains mucosa and submucosa only, rather than all 4 layers as a true diverticulum does) occurs in the neck between the cricopharyngeus and the thyropharyngeus.

Malrotation of the gut results in the duodenojejunal flexure to lie to the right (instead of the normal left) of the midline and cecum in epigastrium or right hypochondrium (instead of normal right iliac fossa); a band (of Ladd) runs across the duodenum from right to left and the narrow base of small bowel mesentery predisposes it to volvulus.

Meckel's diverticulum is the commonest anomaly of the GI tract. It is a remnant of the vitelline (omphalomesenteric) duct and is located in terminal ileum about 2 feet from the ileocecal junction.