Abstract Infectious diseases of the gastrointestinal tract can be broadly divided into three morphological categories: (1) non-specific active infectious bacterial colitis caused by infectious agents such as Campylobacter , Shigella or Salmonella , (2) specific histopathological changes such as Cytomegalovirus colitis, or colitis associated with Mycobacterium avium intracellulare infection and (3) minimal inflammatory mucosal changes, such as those seen with microsporidiosis and intestinal spirochaetosis. Recognising these three general patterns of inflammation, while reviewing gastrointestinal biopsies, may facilitate their diagnosis and differential diagnosis.