An introduction to gastrointestinal pathology

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Micrograph of a tubular adenoma, a very common diagnosis in gastrointestinal pathology. H&E stain.

Gastrointestinal pathology, also gastrointestinal tract pathology, is a large part of pathology as radiologists can often describe the extent of disease... but don't get the diagnosis right all the time.

Cytopathology of the gastrointestinal tract is dealt with in the gastrointestinal cytopathology article.



Layers of the stomach. (WC)

Layers of the alimentary canal:[1][2]

  • Mucosa (epithelium, lamina propria, muscularis mucosa).
  • Submuscosa and submucosal plexus (or Meissner's plexus).
  • Muscularis externa (inner longitudinal, myenteric plexus (or Auerbach's plexus) outer circumferential).
  • Adventitia (if retroperitoneal), serosa (if intraperitoneal).

Cell types

  • Goblet cells.
    • Secrete mucin.
  • Enterochromaffin cells, AKA Kulchitsky cells.
    • Subnuclear eosinophilic granules.
      • Serotonin.
  • Paneth cells.
    • Supranuclear eosinophilic granules.

Memory device:

  • Supranuclear granules = paneth cell.




Small bowel

  • Villi - should see three good ones in a normal biopsy.
  • Crypts.
  • Paneth cells.
  • Goblet cells.
    • Few in proximal small bowel (duodenum).
    • Abundant in distal small bowel (ileum).


  • Small bowel (as above).
  • Submucosal glands (Brunner's glands).

Large bowel versus small bowel

  • Small intestine.
    • Villi (key feature).
    • Brunner's glands - duodenum only (key feature).
    • Paneth cells more common.
      • Paneth cells are in the base of the crypts and have eosinophilic granules. They are found (normally) in the small bowel and right colon. They may appear on the left side (i.e. descending colon) in pathologic states, e.g. IBD.
  • Large intestine
    • More goblet cells.
    • More lymphocytes usually.

Cecum versus rectum

  • Cecum.
    • Less goblet cells - more absorptive cells.[3]
    • More inflammation (plasma cells, eosinophils, lymphoid aggregates).[3]
    • Paneth cells.
  • Rectum.
    • More goblet cells.
    • No Paneth cells normally.

DDx by location

A short DDx for location of abnormality:

  • Lumen:
  • Surface of epithelium:
  • Infiltration of epithelium:
  • Epithelial architeture:
    • Serration - SSA, hyperplastic polyp.
    • Increased lamina propria/loss of crypts - IBD, juvenile polyp).
    • Distortion - IBD, infection, ischemia.
    • Crypt branching - IBD, ischemia, chronic infection, SSA.
    • Back-to-back glands - malignancy, dysplasia.
  • Single cell infiltrates - lamina propria:
    • Epithelial - signet ring cell carcinoma.
    • Macrophages - MAI, TB, Whipple disease, Yersinia.
  • Nuclear abnormalities:
    • Pseudostratification - repair, dysplasia, malignancy.
    • Nuclear enlargement - malignancy, viral cytopathic effect.
  • Submucosal:
    • Brunner's gland - duodenum.
    • Fibrosis - IBD, prolapse.
    • Nests - neuroendocrine tumours.

Luminal gastroenterology


Intestinal polyps

The bread and butter of gastrointestinal pathology.



Largely forgotten organ at SB... but no shortage of these at SMH.


H. pylori, cancer and more...

Small bowel

The part of the GI tract that pathology has mostly forgot. Crohn's disease is dealt with in a separate article.


Commonly biopsied. Celiac... cancer... giardia?


The first part of the large intestine. Technically, it is not part of the colon.


It hangs off the cecum. Commonly, it comes to the pathologist because of acute appendicitis.


Colorectal tumours are dealt with in colorectal tumours. Crohn's disease and ulcerative colitis are dealt with in the inflammatory bowel disease article. Includes discussion of the rectum. The anus is a separate article.

Accessory organs of the gastrointestinal tract


A growth industry... with the expanding waist lines in the (Western) world.


An organ that pathologists now sometimes forget. There are separate articles for the medical liver diseases, liver neoplasms and liver transplantation pathology.


An organ that is occasionally afflicted by cancer. It is primarily seen in large centers where they do ERCPs and Whipples.

Pathology (detail articles)

Inflammatory bowel disease

The bread and butter of gastroenterology and GI pathology.

Gastrointestinal stromal tumour

The most common GI stromal tumour.

Graft-versus-host disease

An uncommon thing that complicates bone marrow transplants.

Eosinophilic enterocolitis

Pneumatosis intestinalis

Pneumatosis cystoides intestinalis

See also


  1. URL:
  2. URL:
  3. 3.0 3.1 Mills, Stacey E. (2006). Histology for Pathologists (3rd ed.). Lippincott Williams & Wilkins. pp. 633. ISBN 9780781762410.

External links