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Histology of the lower digestive tract

The upper gastrointestinal (digestive) tract (GIT) has the responsibility of breaking food down from its macromolecular form, to its comprising monomeric units. In the lower GIT, these monomers are transported from the lumen of the digestive tube to the surrounding vascular system.

They are then delivered to the hepatic system for further processing and subsequent distribution to target cells. For the purpose of absorption, there are several histological differences between the upper and lower GIT.

From the duodenum to the anus, the GIT has been modified to increase its ability to absorb water and nutrients from its lumen as it propels its indigestible contents towards the anus for expulsion. This article will look at the histological composition of the small intestines, large intestines (colon), rectum and anus. Associated histopathologies will also be briefly covered.

  1. Small intestine
    1. Course
    2. Histology
  2. Large intestine
    1. Course
    2. Histology
  3. Rectum and anus
  4. Clinical aspects
  5. Sources
+ Show all

Small intestine


Small intestine (anterior view)

This seven meter long tube, comprising the duodenum, jejunum and ileum, is the longest portion of the alimentary canal. The small intestine commences its convoluted course through the abdomen at the wider pyloroduodenal sphincter and terminate at the more narrow ileocecal valve.

Although there aren’t many anatomical demarcations that distinguish between the segments of the small intestines, there are histological differences that allow the observer to recognize transition points between them.


The general layout of the small intestine is similar to the four-layered outline of the stomach, and follows throughout the distal GIT.

The mucosa, which is lined by simple columnar epithelium, projects serially along the length of the small intestines to produce a “hills and valleys” appearance. The “hills” represent the villi, which are permanent finger-like projections.

The villi increase the surface area of the intestines, which subsequently increases its absorptive capacity. The villi also become decreasingly prominent towards the distal end of the small intestine. Centrally, each villus has a core of connective tissue in which neurovascular, lymphatic and smooth muscular structures course.

The villi’s lamina propria has, in addition to neurovascular and lymphatic structures, a myriad of immunocompetent cells that aid in protecting the body from pathogenic invasions. Between neighbouring villi, are “valleys” known as the crypts of Lieberkühn (intestinal glands).

Enteroendocrine, Paneth, absorptive, goblet and stem cells are located in these depressions. The space is continuous with the epithelial lining of the villi and provides a communicative pathway between the cells of the lamina propria and the intestinal lumen.

The lumen of the small intestines also has visceral folding of the mucosa that is analogous to the stomach’s rugae. However, these plicae circulares are permanent foldings and as such, they do not disappear with intestinal distention. The muscularis mucosae also projects into the villi to facilitate motility and food-villi interactions.

The lymphatics, cells and glands of the small intestines can be separated into two groups: those found throughout the length of the small intestines and those restricted to one of the three areas.

Those found throughout the small intestines include:

  • Tall columnar absorptive cells that reside in the crypts of Lieberkühn and are equipped with microvilli;
  • Mucous secreting goblet cells dispersed between absorptive cells;
  • Undifferentiated stem cells that replace the other cells after they become non-functional or worn;
  • Eosinophillic, lysozyme secreting Paneth cells at the base of the crypts of Lieberkühn that provide antibacterial and phagocytic activity; and
  • Hormone secreting enteroendocrine cells that regulate the secretion of pancreatic, biliary and gastric juices and activates enteric motility.
Goblet cells (histological slide)

Each of the three parts of the small intestines has glands and cells that are exclusively located in that area:

  • The duodenum has light-staining, branched, tubuloacinar Brunner’s glands proximally in its submucosa that secretes its contents as a protective response to the presence of acidic chyme;
  • In the distal ileum, lymphatic aggregates (called Peyer’s patches) covered with phagocytic M-cells, reside in the submucosa and lamina propria of the region;
  • The jejunum is marked by the absence of Brunner’s glands, and Peyer’s patches. However, the previously mentioned glands are present here.
Peyer's patches (histological slide)

Finally, the small intestines are equipped with an inner circular and an outer longitudinal layer of smooth muscle, collectively classified as the muscularis externa. Located between these muscle layers is the parasympathetic plexus of Auerbach. The outermost parts of the intestines (serosa) are covered by a single-layered squamous epithelium that provide protection for the organ.

Large intestine


Large intestine (anterior view)

The large intestine (colon) commences its course in the right inguinal quadrant as the cecum and vermiform appendix. The wide, sacculated tube travels superiorly, as the ascending colon, and then courses horizontally to the left at the hepatic flexure.

It continues its transabdominal course as the transverse colon until it arrives at the splenic flexure, where it courses inferiorly as the descending colon. In the left inguinal region, it takes an “S”-shaped course as the sigmoid colon before terminating at the rectosigmoidal junction. Along this course, undigested and unabsorbed residues (food, drugs etc) are condensed and converted to faeces by increasing luminal water absorption.


Histologically, the large intestines can be distinguished from the small intestines by the absence of villi, plicae circularis, and Paneth cells (in adults). Simple columnar epithelium lines its mucosa. The crypts of Lieberkühn are deeper in the colon and goblet cells become more abundant and increase in number towards the terminal end of the large intestine.

The enteroendocrine cells are dispersed throughout the mucosa and the surface epithelium is equipped with brush borders. It is also noteworthy that the aggregations of lymph nodules are more solitary that those observed in the small intestines. The double layered muscularis mucosae that is typical of the GIT is also present.

The neurovascular and lymphatic arrangement of the submucosa of the large intestine is also consistent with the rest of the GIT. The muscularis externa has its longitudinal and circular layers present. However, the longitudinal layers concentrate into three muscular bands that course along the length of the colon called the taeniae coli muscles.

Contraction of these taeniae coli in the un-distended colon give rise to the sacculations (haustra) observed grossly. As was previously observed in the small intestines, Auerbach’s parasympathetic plexus is present between the layers of the muscularis externa.

The vermiform appendix has a similar histological appearance to the colon with the following exceptions:

  • The taeniae coli are absent in the appendix;
  • The lamina propria and submucosa contain joining lymphatic nodules along its length;
  • The muscularis externa is continuous circumferentially and longitudinally;
Vermiform appendix (histological slide)

Rectum and anus

The epithelium of the colon is continuous with that of the proximal rectum. Similar to the colon, longer, narrower crypts of Lieberkühn with numerous goblet cells, adipocytes and lymphatic aggregates are also observed in the lamina propria of the rectum. Proximally, in the empty rectum, the presence of the muscularis mucosae creates longitudinal folds that are lined by mucosa and have submucosa centrally.

In the distal rectum and anal canal, the temporary longitudinal folds are replaced by permanent (present even when the anal canal or rectum is full) rectal columns.

The muscularis externa assumes its typical bilayer arrangement along with taeniae coli continuing along its length. As is expected, Auerbach’s plexus courses between the inner circular and outer longitudinal layers of the muscularis externa.

Myenteric plexus (histological slide)

A sharp histological change can be readily seen while transitioning from the rectum to the anal canal. At the anorectal junction, the epithelium changes from simple columnar to stratified squamous. Approaching the anorectal junction, the crypts of Lieberkühn become shorter and more separated from each other.

At the junction, the muscularis mucosae disappear. Lymphatic nodules are present in the lamina propria (which transitions to the dense irregular connective tissue type that is typical of the anal canal). In the upper region of the anal canal, the inner circular muscle layer thickens to form the internal anal sphincter; while distally, smooth muscle is replaced by skeletal muscle that forms the external anal sphincter.

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