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Collagenous colitis is characterized by a conspicuous subepithelial collagenous band (more than 10 micrometer). The collagenous thickening is highlighted by Masson trichrome stains. (The eosinophilic band is negative for amyloid). The inflammatory changes parallel the collagen deposition .

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In lymphocytic colitis there is absence of thickened collagenous layer. 

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In both collagenous and lymphocytic colitis there is an increase in intra-epithelial lymphocytes (more than 20 lymphocytes per 100 epithelial cells  compared to the normal value of 5 lymphocytes per 100 epithelial cells) and a moderate to marked increase in mononuclear cells (plasma cells and lymphocytes) in the lamina propria. Clusters of chronic inflammatory cells are present at the base of the crypts. Some eosinophils and mast cells are often present deep in the mucosa. 

The crypt architecture and goblet cells  are usually well preserved with no cryptitis or crypt abscess formation.  Some cases have been reported  showing minimal crypt architectural  distortion, some goblet cell depletion, presence of neutrophils and focal surface epithelial damage. 

In many of the documented cases of microscopic colitis there are overlapping features of both lymphocytic and collagenous colitis. There is striking histological similarities between coeliac disease and both collagenous and lymphocytic colitis.

Recently non-necrotizing pericryptal granulomas have been described in cases of microscopic colitis. These cases should not be confused with Crohn's disease.

It has been reported that Tenascin is a useful marker in the diagnosis of collagenous colitis.

Note:  Tangential sectioning of normal colon can result in artifactual thickening of the basement membrane. Hence in the absence of the characteristic inflammatory pattern tangentially cut colonic biopsies should not be diagnosed as collagenous colitis.

Some authors have divided  microscopic colitis into

-Classical - collagenous colitis, lymphocytic colitis   and 

-Non-classical - granulomatous colitis, giant-cell microscopic colitis, pseudo-membranous microscopic colitis.

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Microscopic colitis with giant cells: a rare new histopathologic subtype?Int J Surg Pathol. 2004 ;12(1) :45-8.

Sequential clinical and histopathological changes in collagenous and lymphocytic colitis over time.Mod Pathol. 2004;17(4):395-401

Microscopic colitis with granulomatous inflammation.Histopathology. 2004;45(1):82-6.

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Diagnosis and management of microscopic colitis syndrome.J Clin Gastroenterol. 2004;38(5 Suppl) :S27-30.

The terminal ileum is affected in patients with lymphocytic or collagenous colitis.Am J Surg Pathol. 2002 ;26(11):1484-92.

Collagenous colitis: a study of the distribution of morphological abnormalities and their histological detection.Hum Pathol. 1999;30(4):451-7.

Microscopic colitis syndrome: lymphocytic colitis and collagenous colitis.Semin Gastrointest Dis.1999;10(4):145-55.

Collagenous colitis: a practical orientated approach to diagnosis. Adv Anat Pathol. 1999 Nov ; 6(6): 327-31

Tenascin labelling in colorectal biopsies: a useful marker in diagnosis of  collagenous colitis. Histopathology 1999 May; 34(5) : 425-31

Chronic, unexplained diarrhea: are biopsies necessary if colonoscopy is normal?Am J Gastroenterol. 1995 Mar;90(3):372-6.

Collagenous colitis and microscopic colitis: the watery diarrhea-colitis syndrome.Am J Gastroenterol. 1989 Jul;84(7):763-8.

Biopsies of the endoscopically normal rectum and colon; a necessity. Incidence of collagen colitis and microscopic colitis. Gastroenterol.Clin.Biol. 1989; 13(4): 360-363