Integrated Practical – Case 2 and 3   

Stomach and Intestines

Learning objectives:


Practical Information:

General comments on histology:  To distinguish the various parts of the alimentary tract, you will need to pay close attention to the structure and composition of each layer in each specimen studied. See Kierszenbaum’s Histology and Cell Biology Figure 15-7 and/or Wheater's Functional Histology Figure 14.2. In particular, look for differences in the mucosa and submucosa. Also, as you examine each slide look for and learn to identify neurons of the enteric nervous system (both myenteric and submucosal). These will be more prevalent and apparent in some specimens than in others.  You need to be able to identify and differentiate all the different functional areas of the alimentary tract. Try to learn to identify the regions by what structures you see and not by what structures that you do not see!


1. Stomach

Cardio-oesophageal junction Dog H&E Slide 65
Cardio-oesophageal junction Dog Gomori's Trichrome Demo slide

Slide 65 x 40  Slide 65 x 100  Slide 65 x 200  Slide 65 x 200  Slide 65 x 400

Trichrome stain x 100

Examine slide 65 (cardio-oesophageal junction, dog, H&E) and the trichrome-stained demo slide on low power and note the abrupt change in epithelium at the junction between the oesophagus and stomach.

What type of epithelium lines the stomach? Is the stomach epithelium secretory, absorptive or both? What substances does it secrete and/or absorb?



Note the presence of cardiac glands in the lamina propria and take note of the large amounts of lamina propria (connective tissue) between the cardiac glands. Do not confuse the cardiac and oesophageal glands which, although adjacent to each other, are in different layers of the wall.

How would you classify these cardiac glands (e.g. compound tubuloalveolar etc.)? What structure do the glands open into?  What are the small depressions in the surface of the stomach lined by stomach surface epithelium called?

Body of the Stomach Cat H&E Slide 66
Cat Haematoxylin-PAS Slide 67
Fundic stomach Human H&E Demo H7925

Slide 66 x 40  Slide 66 x 40  Slide 66 x 100  Slide 66 x 200  Slide 66 x 400  Slide 66 x 400
Slide 67 x 100   Slide 67 x 400
Slide H7925 x 40

Examine the demonstration slide H7925 macroscopically and identify the folds in stomach.  Also identify the folds on the lumen of the stomach model. These folds involve several layers of the stomach wall. 

What are the name of the folds found in the stomach? What is their function? What layers do they involve? Is there an equivalent in the small intestine and, if so, what are they called there (and do they involve the same layers)?




Examine the body of the stomach slides (slide 66 cat H&E, 67 cat H-PAS, demo H7925 human H&E) at low power and identify all the layers present in the wall. 

How many layers of smooth muscle are there in the muscularis externa, and what is the orientation of each?  Two of the layers are not complete.



In slide 66 examine the mucosa and compare what you see with what was seen in the previous slide 65 from the cardiac region. Note particularly the depth of the gastric pits (they should be shallow - about 10 - 20% of the depth of the mucosa), the complexity of the gastric glands and the small amount of lamina propria (loose connective tissue) between the glands.  These glands (and the area of stomach in which they are found) are often described as peptic glands (of the peptic stomach).


In slide 67 what substance has the PAS stained? Which cells have been stained?



Examine slide 66 at high power and see if you can identify the gastric pits and the two divisions of the gastric gland.


There are four functionally different cell types found in the glands:

(1) Mucus Neck Cells

(2) Chief or Peptic Cells

(3) Parietal or Oxyntic Cells

(4) Enteroendocrine cells


With the help of your text book see if you can identify, in your slide, these different cell types. You should be aware of the ultrastructural characteristics of these different cell types, as shown in the demonstration electron micrographs. 

What is the distribution of these cells within the glands?  What are the functions of these four types of cell?


Pyloric stomach Cat H&E Slide 66b
Pyloric stomach Human H&E Demo H7950

Slide 66b x 100  Slide 66b x 200  Slide 66b x 400
Slide H7950 x 100

Examine the slides of the pyloric region of the stomach.  Note the greater depth of the gastric pits (approximately 50% of the mucosal depth) compared to the body of the stomach (10 - 20% of depth) and the coiled nature of the glands. The cells of the pyloric glands mainly secrete mucous rather than the digestive enzymes that were secreted by the body and fundic regions of the stomach.

What other secretory cells would you expect to find in this region of the stomach?



You should revise the mechanisms that control gastric secretion and motility. Revise also the interaction of control between the stomach and the small intestine.



2. Small intestine histology

Pyloro-duodenal junction (L.S.) Cat H&E Slide 68
Small Intestine (T.S.) Cat H&E Slide 69
Duodenum Human H&E Demo H8000

Slide 68 x 40  Slide 68 x 100
Slide 69 x 100  Slide 69 x 400  Slide 69 x 400
Slide H8000 x 40


Because of the way the block for Slide 68 has been cut it may be difficult to orientate yourself.  Using x4 objective, locate the junction of the gastric (pyloric) mucosa and the intestinal mucosa. It is clearly identifiable by the abrupt transition from gastric pits to intestinal villi. Compare the pylorus and the duodenum with regard to the composition of their various layers (mucosa, submucosa, muscularis externa). Identify:

1. Goblet cells in the intestinal epithelium of the duodenum (are there any in the stomach?)

2. The position of the pyloric glands and intestinal glands (or crypts of Lieberkuhn) in the lamina propria

3. Brunner's glands in the submucosa of the duodenum

4. External muscle layers

5. Note the way in which the Brunner's glands may also be found in the submucosa below the last of the pyloric stomach.

6. Note also that the tunica muscularis is greatly developed in this junctional region.


Using x10 objective and Slide 68, select and examine a field showing penetration of the mucosal muscle by ducts of Brunner's glands and their drainage relation to the crypts of Lieberkuhn. (Brunner's glands secrete neutral or slightly alkaline mucous and lie in the submucosa). Brunner's glands are much less prevalent in the distal duodenum. 

Explain the presence of these Brunner's glands at the junction of the stomach and the small intestine.  What other secretion released in this area has a similar function? 


Where else in the gastrointestinal tract might you see submucosal glands? 



Why would the muscularis externa be of increased thickness and complexity at the junction of the pyloric stomach and the duodenum?



Using Slides 68 and 69 examine a field showing villi cut in longitudinal section. Note the broad duodenal villi and the straight crypts of Lieberkuhn (tubular glands) extending from the base of the villi to the thin mucosal muscle. Because of the plane of section these crypts may be cut in a number of different profiles. 

What would be the equivalent of the crypts in the stomach?  Which cells in the crypts produce secretin and CCK?  What is the function of secretin and CCK?



The lamina propria (loose connective tissue) is very cellular and contains many lymphocytes. In the core of villi, strands of smooth muscle, which are extensions of mucosal muscle, follow the course of the lacteals.  Each villus also has an extensive capillary bed.

Why is there an extensive capillary bed in each villus?



The epithelium of the villi and crypts consists of absorptive cells, mucous secreting goblet cells, enteroendocrine cells and in the bottom of crypts, Paneth cells. The principal cell in the crypt is the undifferentiated columnar cell which has a pale basophilic cytoplasm. It divides frequently and differentiates into the other epithelial cells described. Using your text book and the micrograph below note the EM features of some of these cells and view the transmission electron micrograph of an enteroendocrine cell.

Enteroendocrine cell EM x 3500


Jejunum Cat Alcian Blue/Weigert's Slide 70
Ileum Cat H&E Slide 76
Ileum Human H&E Demo H8075
Jejunum Human H&E Demo H8050

One of the main functions of the small intestine is absorption of digested foodstuff and water. Because of this the surface area of the small intestine has been greatly increased (x600). You have already identified villi. Now look for the brush border (microvilli) on the surface of the absorptive cells (Slide 69) and plicae circulares (folds of the wall that have a core of submucosal connective tissue). Note that the lamina propria (loose connective tissue) forms the core of intestinal villi and that the submucosa, a richly vascularised and innervated denser connective tissue forms the core of a plicae circulares.

Brush border EM x 22 500

What would be the equivalent of a plicae circulares in the stomach?
What is the ultrastructural and functional difference between a microvillus and a cilium?
What is the glycocalyx and where would you find it?
Explain why you’d expect the glycocalyx in the small intestine to be quite pronounced.

Goblet cells are specifically demonstrated in slide 70; their mucus content (acid mucopolysaccharide) is stained selectively by alcian blue. Review the ultrastructural features of a goblet cell below, while using your text books note any other EM features of goblet cells. Note the absence of glands in the submucosa of the jejunum and ileum.

Slide 70 x 100  Slide 70 x 200  Slide 70 x 400

Goblet cell x 1000

Goblet cell EM x 3500

What specialisations have you seen in these sections of the small intestine that would improve the functions and efficiency of the small intestine?


The entire length of the gastrointestinal system is in fact an interface between the internal and external environments. For this reason it (like the respiratory system) has elements of the immune system associated with it. This may take the form of individual lymphocytes or aggregations of lymphocytes in diffuse or nodular form (MALT). In slides 69 and 70, using the x40 objective, examine the lining epithelium and look for lymphocytes. These can be identified by their small round darkly stained nuclei usually in a position apical to the epithelial cell nuclei.


Look also for large aggregations of lymphocytes, in diffuse and nodular form, which may extend from the submucosa through the mucosal muscle into the mucous membrane. Note: Lymphoid aggregations are not present in all sections - so if you can't see them in your section, borrow a slide from another student. Such lymphocytic masses are a constant feature of the ileum and are known as 'aggregated nodules' or Peyer's patches (See slide 76 or the demonstration slide). These patches have efferent lymphatic vessels only. In slide 76 the glands (crypts of Lieberkuhn) and mucosal muscle are distorted where they have been infiltrated by diffuse and nodular lymphocytic tissue.



3. Large intestine

Appendix T.S. Monkey H&E Slide 71
Appendix Human H&E Demo H8100

Slide 71 x 100  Slide 71 x 200
Slide H8100 x 40

Examine the sections of the appendix (slide 71 t.s. monkey H&E, demo H8100 human H&E) and note that the crypts and the muscularis mucosa are poorly developed and have been infiltrated by lymphatic material. The submucosa is well developed and contains blood vessels and adipose tissue. The external muscle coat also appears to be reduced. Note the presence of nodules and germinal centres.  The appendix is one of the few sites in the alimentary system where there are permanent aggregations of lymphoid material (the ileum being one of the others).

Large Intestine T.S. Cat PAS/Haem. Slide 72
Colon Human H&E Demo H8106

Slide 72 x 100  Slide 72 x 400
Slide H8106 x 100  
Slide H8106 x 100   Slide H8106 x 100  

Examine the slides of the large intestine (slide 72 t.s. cat PAS/Haem and/or demo H8106 human H&E). Look at the appearance of the glands, the cells present in the glands, presence or absence of villi, etc. Note that in the cat slides the outer layer of the muscularis externa is NOT arranged as taenia coli as described for humans. The glands are straight tubular glands that extend from the surface to the muscularis mucosa. The two main cell types present in the glands are columnar absorptive cells and goblet cells. There are no villi.

Does the large intestine look more like the stomach or small intestine? Why? How would you tell them apart?  Has there been any change in the numbers of goblet cells as we move down the gut?

Rectum Cat H&E Slide 73

Slide 73 x 40  Slide 73 x 400


Examine the slide of the rectum (73, cat H&E).  The mucous membrane is thrown into large folds. The crypts (intestinal glands) are the longest of the entire intestine (0.7 mm). Look closely at the muscularis mucosa and note the well developed mucosal muscle which has an inner circular and outer longitudinal coat (you will have to search for this with the x40 objective).


Anorectal Junction Pig H&E Demo H8109

Slide H8109 x 40  Slide H8109 x 200

Examine the slide of the anorectal junction (demo H8109, pig H&E) and note the epithelial transition region (simple columnar to stratified squamous) and also the glandular tissue buried in the muscularis in the vicinity of the anorectal junction. Look carefully at the increased muscle of the muscularis externa for evidence of skeletal muscle (external anal sphincter) and smooth muscle (internal anal sphincter).


Anus H&E Demo 99-8110

Slide 99-8110 x 40   Slide 99-8110 x 100

Examine the slide of the anus (demo 99-8110, human H&E) and note the stratified squamous epithelium and any evidence that this region is keratinised (stratum corneum; integumentary system glands). 

Is the anal epithelium cornified?  Where else in the GIT would you find muscular sphincters?