GI Tract Lab

Learning Objectives

  • Describe the histological characteristics of the layers comprising each segment of the gastrointestinal tract and describe how they relate to their function
  • Name and describe four transitional junctions in the GI tract
  • Describe the topography of the gastric gland, its component cells, and architectural differences between glands in the three regions of the stomach
  • Describe the structure of the small intestine, how its surface area is maximized, and the cells that comprise its epithelium
  • Contrast the histological appearance of the large intestine from that of the small intestine
  • Identify a few key pathological examples regarding the GI tract


  • mucosa
  • epithelial cell layer
  • lamina propria
  • muscularis mucosa
  • submucosa
  • muscularis externa
  • inner circular layer
  • outer longitudinal layer
  • adventitia
  • mesothelium
  • serosa
  • protective mucosa
  • secretory mucosa
  • absorptive mucosa
  • absorptive/protective mucosa
  • gastro-esophageal junction
  • gastro-duodenal junction
  • ileo-cecal junction
  • recto-anal junction
  • voluntary muscular action
  • peristalsis
  • mass movements
  • enteric nervous system
  • interstitial cells of Cajal
  • Meissner's (submucosal) plexus
  • Auerbach's (myenteric) plexus
  • oral cavity
  • tongue
  • esophagus
  • stratified squamous epithelium
  • stomach
  • chyme
  • gastric glands
  • gastric pit
  • isthmus
  • neck
  • base
  • mucous-secreting cells
  • parietal cells
  • tubulovesicular system
  • membrane canaliculi
  • chief cells
  • enterochromaffin-like (ECL) cells
  • G-cells
  • stem cells
  • cardia
  • body
  • pylorus
  • small intestine
  • plicae circularis
  • villi
  • lacteal
  • microvilli
  • duodenum
  • glands of Brunner
  • jejunum
  • ileum
  • Peyer's patches
  • crypts of Lieberkuhn
  • enterocytes
  • goblet cells
  • Paneth cells
  • large intestine
  • feces
  • tenia coli
  • appendices epiploicae
  • appendix
  • rectum
  • anus

Pre-Lab Reading


The digestive system is responsible for the ingestion and digestion of dietary substances, the absorption of nutrients, and the elimination of waste products. The secretions of the associated glandular organs, such as the salivary glands, pancreas, liver, and gall bladder, aid the GI tract in accomplishing these functions. This laboratory will focus on the sequential segments of the gastrointestinal tract; the subsequent laboratory will focus on the glandular organs.

Basic Organization of the Gastrointestinal Tract

The GI tract is a muscular tube lined by a mucous membrane and features a basic histological organization that is similar across all of its segments of the tract. Several distinct, concentric layers line each segment of the tract:

  • The mucosa surrounds the lumen of the GI tract and consists of an epithelial cell layer supported by a thin layer of connective tissue known as the lamina propria. The muscularis mucosa is a thin layer of smooth muscle that supports the mucosa and provides it with the ability to move and fold.
  • The submucosa is a thick connective tissue layer that contains arteries, veins, lymphatics, and nerves.
  • The muscularis externa surrounds the submucosa and is composed of two muscle layers, the inner circular layer and outer longitudinal layer. These two layers move perpendicularly to one another and form the basis of peristalsis.
  • The adventitia consists of connective tissue containing blood vessels, nerves, and fat. In the portions of the tract within the peritoneal cavity, it is lined by the mesothelium. Recall from the Laboratory on Epithelia that the mesothelium is a specially named layer of simple squamous epithelial cells. In these tissues, the adventitia is referred to as serosa.

These four layers can be identified in most gastrointestinal segments, although different segments demonstrate important structural variations that can provide clues to their functions. The greatest structural variations occur in the mucosal layers. There are four distinct types of mucosal variations:

  • Protective mucosa is characterized by a stratified squamous epithelium. It is found in the oral cavity, pharynx, esophagus, and anal canal.
  • Secretory mucosa contains cells that are responsible for the secretion of digestive enzymes. It is found exclusively in the stomach.
  • Absorptive mucosa contains two key structures, crypts and villi, and is responsible primarily for absorbing digested nutrients. It is found along the entirety of the small intestine.
  • Absorptive/protective mucosa specializes in water absorption and mucous secretion. It is found in the large intestine.

There are four junctions in the GI tract that are characterized by abrupt changes in the mucosal lining: the gastro-esophageal junction, the gastro-duodenal junction, the ileo-cecal junction, and the recto-anal junction.

Gastrointestinal Motility

In Physiology, you will study the movement of food through the GI tract in detail. For now, it is important to understand a few basic principles and to relate them to the histological structure of the digestive system.

In the first portion of the GI tract, from the oral cavity to the upper esophagus, food moves by voluntary muscular action. In the following portion, from the lower esophagus through the large intestine, food moves by peristalsis. Material moves through the rest of the tract by mass movements, which transport tract contents over long distances.

The motility of the GI tract is accomplished via a diffuse neuroendocrine system that involves the autonomic nervous system and hormones. The enteric nervous system is composed of several groups of nerve cells:

  • The interstitial cells of Cajal serve as the pacemaker cells of the GI tract and are modulated by the parasympathetic nervous system.
  • The submucosal plexus, or Meissner's plexus, is located in the submucosal layer and controls the mucosal glands and the muscularis mucosa.
  • The myenteric plexus, or Auerbach's plexus, is located between the two layers of the muscularis externa and is responsible for peristaltic movements.

With this understanding of the basic structural features of the GI tract, we will now take a more focused look at different portions of the tract. Be sure you understand the function of each portion of the tract before you study the structure in detail in the Laboratory Slides.

Oral Cavity and Esophagus

Food enters the digestive tract in the oral cavity, where it is masticated into particles on which digestive enzymes can act more efficiently. In the mouth, food particles are mixed with saliva, which lubricates them and initiates their digestion. The salivary glands will be discussed in detail in the next laboratory.

The tongue is a muscular organ covered by oral mucosa that manipulates the food and contains the sensory organs for taste. The taste buds will be discussed in detail in the Laboratory on Sensory Systems.

The esophagus is a muscular tube that transports food from the pharynx to the stomach. It is lined by a stratified squamous epithelium and has a prominent muscularis mucosa and thick muscularis externa. The muscularis externa of the esophagus is unique in that it transitions from striated to smooth muscle over the length of the tube. The esophagus ends in the gastro-esophageal junction.


The stomach is the site where food is mixed with gastric juice and reduced to a fluid mass called chyme. The layers of the stomach wall follow the basic plan described above. The gastric glands are the basic structure of the stomach wall and can be thought of as tiny pits, or indentations, lined by epithelial cells. Gastric glands are structured as a gastric pit that opens into the lumen, followed by an isthmus, neck, and base.

There are several types of cells that are important in producing stomach secretions:

  • Mucous-secreting cells produce mucous and bicarbonate ions, which protect the stomach epithelium from the damaging effects of stomach acid. They appear pale and contain obvious mucous droplets. These cells are located in all layers of the gastric gland, but are particularly prominent in the gastric pit and in the neck of the glands.
  • Parietal cells secrete hydrochloric acid and intrinsic factor, which is important for the absorption of vitamin B12 in the terminal ileum. They have a characteristic pyramidal shape and are usually found in the isthmus of the gastric gland. Parietal cells have a characteristic tubulovesicular system that fuses with their membrane canaliculi when they become activated.
  • Chief cells produce pepsinogen, which is stored in large apical secretory granules. After pepsinogen is secreted, it is converted by the acidic environment of the stomach to pepsin that is an active protease. Chief cells are found in the base of the gastric glands.
  • Enterochromaffin-like (ECL) cells produce histamine, which is important in the release of stomach acid. They are typically found in the base of the gastric glands.
  • G-cells secrete the peptide hormone gastrin into the blood stream.
  • Stem cells divide to replace the other cells in the gastric glands. They are located primarily in the neck of the glands.

The three different regions of the stomach are distinguished on the basis of the histological characteristics of the mucosal glands:

  • The cardia is a circumferential ring about 3 centimeters deep distal to the gastro-esophageal junction. Its glands tend to be convoluted and are lined primarily by mucous-secreting cells.
  • The body is the main part of the stomach and is bounded by the greater and lesser curvatures. Its glands are straight with limited branching and are lined by a smaller population of mucous-secreting cells than those of the cardia. It also contains chief and parietal cells.
  • The pylorus is the distal third of the stomach and terminates at the beginning of the duodenum. It possesses glands with deeper pits and large amounts of coiling and branching. These glands contain many mucous-secreting cells, ECL cells, and G-cells.

The muscularis externa of the stomach is notable because it contains an additional muscular layer. It is structured with inner oblique, middle circular, and outer longitudinal layers. This structure allows for the churning movements that mix the chyme and expose it to the acidic gastric juice produced by the stomach glands.

Small Intestine

The small intestine is responsible for the continued digestion and absorption of the GI tract contents. Reflecting its absorptive function, the surface of the small intestine is amplified significantly at three levels:

  • At a gross level, the small intestine is a long tube into whose lumen projects the plicae circularis, circular folds of the mucosal epithelium, lamina propria, muscularis mucosa, and submucosa.
  • Villi, finger-like projections involving only the epithelium and lamina propria, project into the lumen. They have a central lymphatic vessel known as a lacteal, which is crucial for the absorption of lipids from the intestine.
  • Microvilli make up a brush border on the surface of the columnar cells of the mucosal epithelium.

The small intestine begins after the gastro-duodenal junction and is divided into three segments:

  • In the duodenum, pancreatic juice and bile are released into the lumen. Digestion is completed by enzymes in the pancreatic juice and on the surface of the epithelial cells where the products of digestion are absorbed. The glands of Brunner, extensive mucous glands that are found in the submucosa, are found exclusively in this segment. The villi of the duodenum are also exceptionally long.
  • The jejunum is the site of a great deal of nutrient absorption and has the most prominent plicae circularis.
  • The ileum has the shortest villi and is the site of vitamin B12 absorption. It is characterized by abundant Peyer's patches, which are clumps of diffuse lymphoid tissue, in the submucosa.

The intervening depressions between the villi are known as crypts of Lieberkuhn and can be thought of as the intestinal analogs of the gastric glands. They contain several important cell types:

  • Enterocytes are the tall columnar epithelial cells that make up most of the intestinal lining and perform most of the intestinal digestive and absorptive functions.
  • Goblet cells store and secrete mucous.
  • Paneth cells serve an immune function and are found at the base of the crypts.
  • Enteroendocrine cells produce hormones that govern motility and secretion, just as they do in the stomach.
  • Stem cells replenish the other cell types and are found at the base of the crypts.

The small intestine ends with the ileo-cecal junction.

Large Intestine

The large intestine absorbs water and concentrates waste material that is formed into feces. It lacks villi and contains a disproportionately large number of goblet cells. The lamina propria has many macrophages, plasma cells, eosinophils, and lymphoid nodules. The muscularis externa does not have a continuous longitudinal muscle layer, but instead has three thick bands of muscle called the tenia coli. A thick layer of serosa is present and contains pendulous tabs of adipose tissue called appendices epiploicae.

The appendix is a vestigial organ located near the ileo-cecal junction. It shows the same basic organization as the rest of the large intestine, but has particularly abundant lymphatic nodules.

The large intestine feeds into the rectum, which stores the feces and has a columnar epithelium with abundant goblet cells. Feces pass out of the rectum, through the anus, and out of the body. The anus is characterized by a stratified squamous epithelium that undergoes a gradual transition to skin containing sebaceous and apocrine sweat glands.

Pre-Lab Quiz

  1. Describe the changes in epithelial structure at each of the following four junctions in the GI tract:
    • gastro-esophageal
    • gastro-duodenal
    • ileo-cecal
    • recto-anal
  2. What are the four types of gastrointestinal mucosa, and what are their key characteristics?
  3. Answer:
  4. What are the two plexuses of the enteric nervous system and which muscular layers do they control?
  5. Answer:
  6. Match the cell type with its secretion:
  7. 1. Goblet Cell A. gastrin
    2. Parietal Cell B. histamine
    3. Chief Cell C. pepsinogen
    4. G-cell D. intrinsic factor
    5. ECL Cell E. mucous


Please select whether to view the slides in study mode or quiz mode. In study mode, the images will contain labels and a description. In quiz mode, labels and description will be hidden.

  1. Esophagus
  2. Gastro-Esophageal Junction
  3. Stomach
  4. Gastric Gland
  5. Stomach Cardia
  6. Stomach Body
  7. Stomach Pylorus
  8. Parietal Cells
  9. Chief Cells
  10. Duodenum
  11. Jejunum
  12. Ileum
  13. Villus
  14. Crypts of Lieberkuhn
  15. Colon
  16. Recto-Anal Junction
  17. Auerbach's Plexus
  18. Meissner's Plexus

Virtual Microscope Slides

  1. Esophagus
  2. Under low power, locate the stratified squamous epithelium surrounding the lumen. Describe how the cells change in shape from the basal to apical layer of this epithelium. Is keratin visible in this slide?
  3. Stomach
  4. Under low power, identify the layers of the stomach wall. From which portion of the stomach is this slide most likely taken?
  5. Jejunum
  6. Identify the three characteristics of the small intestine that maximize its surface area: plicae circularis, villi, and microvilli.
  7. Ileum
  8. The ileum has fewer plicae circulares than the jejunum but still has villi. Most of these villi are seen in cross section. Identify the luminal space, the cells that comprise the villus epithelium, and the tissue found in the center of each villus.
  9. Colon
  10. Identify the layers of the colon wall, and contrast the structure of the colon epithelium with that of the small intestine. How does the number of goblet cells change?


Please select whether to view the slides in study mode or quiz mode. In study mode, the images will contain labels and a description. In quiz mode, labels and description will be hidden.

  1. Barrett's Esophagus
  2. Celiac Disease
  3. Ulcerative Colitis


  1. Name this structure.
  2. Answer: Esophagus
  3. Name the junction.
  4. Answer: Esophageal-Gastric Junction
  5. What part of the stomach is this?
  6. Name the cell type and identify its major secretion.
  7. Answer: Parietal cell - HCl
  8. Name the cells bordering the lumen.
  9. Answer: Paneth Cell
  10. What region of the GI tract is this?
  11. Answer: Small Intestine - Duodenum. Note the presence of Brunner's Glands in the submucosa.
  12. Name this region of the intestine.
  13. Answer: Jejunum. Note the presence of plicae circulares.
  14. What characterizes this region of the intestine.
  15. Answer: Peyer's Patches
  16. In this cross section through the center of a villus, identify A, B, C, D, and E.
  17. Answer: A = enterocyte brush border, B = lacteal, C = goblet cell, D = immune cells (lymphocytes), E = lamina propria
  18. GI motility is compromised in Hirschprung's disease, which results from the incomplete formation of the myenteric plexus. What differences would you expect to see when you compare a histological specimen from a region of the colon with Hirschprung's with a normal region?
  19. Answer: The region with Hirschprung's will lack the myenteric plexus neurons typically visible between the two layers of the muscularis propria. If the submucosal plexus is still intact, those neurons should still be visible.