In histology, cryptitis refers to inflammation of an intestinal crypt. Cryptitis. H&E stain.Focal cryptitis and a granuloma. H&E stain.Focal cryptitis and a granuloma. H&E stain. In histology, cryptitis refers to inflammation of an intestinal crypt. Cryptitis is a non-specific histopathologic finding that is seen in several conditions, e.g. inflammatory bowel disease, diverticular disease, radiation colitis, infectious colitis.