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Changes in the composition of the intestinal microbiota are an important environmental factor in the development of IBD.Detrimental changes in the intestinal microbiota induce an inappropriate (uncontrolled) immune response that results in damage to the intestinal epithelium.In this case, a diagnosis of indeterminate colitis may be made.Although a recognised definition, not all centres refer to this.Crohn's disease affects the small intestine and large intestine, as well as the mouth, esophagus, stomach and the anus, whereas ulcerative colitis primarily affects the colon and the rectum.In spite of Crohn's and UC being very different diseases, both may present with any of the following symptoms: abdominal pain, vomiting, diarrhea, rectal bleeding, severe internal cramps/muscle spasms in the region of the pelvis and weight loss.However, ulcerative colitis can in most cases be cured by proctocolectomy, although this may not eliminate extra-intestinal symptoms. Alternatively, a pouch can be created from the small intestine; this serves as the rectum and prevents the need for a permanent ileostomy.A small percentage of patients with ileo-anal pouches do have to manage occasional or chronic pouchitis.

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Microscopically, ulcerative colitis is restricted to the mucosa (epithelial lining of the gut), while Crohn's disease affects the full thickness of the bowel wall ("transmural lesions").

In the figure beside, there is a NOD2-focused cluster in the causal gene sub-network.

The diagnosis is usually confirmed by biopsies on colonoscopy.

At some point after the first surgery, Crohn's disease can recur in the healthy parts of the intestine, usually at the resection site.

(For example, if a patient with Crohn's disease has an ileocecal anastomosis, in which the caecum and terminal ileum are removed and the ileum is joined to the ascending colon, their Crohn's will nearly always flare-up near the anastomosis or in the rest of the ascending colon).

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