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The Upper Gastrointestinal Tract

The upper gastrointestinal tract (or GI) includes the esophagus, the stomach and the upper small intestine (the duodenum). The esophagus carries food from the mouth to the stomach, where food is partially digested. Crohn’s disease affecting the upper gastrointestinal tract as not as common as in the lower small intestine, but can occur. Scarring and narrowing of the esophageal tract due to inflammation may affect swallowing and increase the likelihood of choking. Fistulas, or perforations, can develop in the stomach, which can allow stomach contents to seep into the abdominal cavity itself.

Crohn’s disease occurs most often in the lower small intestine, where the partially digested food from the stomach and upper small intestine undergoes further digestion before being passed into the large intestine.

Ileum: The ileum is the portion of the small intestine that connects it to the large intestine and is the most common location for Crohn’s. Due to its proximity to the appendix, some people mistake the pain of Crohn’s disease for appendicitis.

The Large Intestine

The large intestine is the next to last section of the gastrointestinal system. The large intestine is where feces are formed. It is comprised of the colon and the rectum. The colon finishes the digestive process and forms stools, which are then stored in the rectum. The large intestine, like the ileum, is a common target for Crohn’s disease.

The anus is the end of the gastrointestinal system. It is the opening where stool is expelled from the body. The anus is a common location for fistula to occur.

Gastrointestinal Skip Areas

Crohn’s may strike different areas of the gastrointestinal tract. For instance, Crohn’s may affect areas of the ileum and the colon, with normal areas between the affected sites. The healthy areas between areas of inflammation are commonly referred to as “skip areas.”

Fibrosis (Scarring)

Chronic inflammation may lead to fibrosis, or the scarring and narrowing of the gastrointestinal tract. Narrowed areas make the possibility of intestinal blockages more likely.


The deep ulcerations caused by the condition may lead to fistulas: Abnormal connections or pathways between structures. Should such ulcers penetrate the intestinal walls, intestinal contents may escape into surrounding tissues. Fistulas often occur around the rectum, and can lead to rectal contents seeping into the bladder, the vagina or even through the skin.

The Mucosa

The mucosa is the innermost layer of the intestinal wall and lines the intestinal tract. The mucosa absorbs nutrients from digested food.


The middle layer of the intestines is composed of muscle, which contracts rhythmically to push food through the digestive tract.


The outer layer of the intestinal tract is called the serosa. Its outer surface is smooth and slippery and prevents the intestines from sticking to one another and other organs within the abdominal cavity.


American Society of Colon and Rectal Surgeons. (updated 1996). Crohn’s Disease.

Carson-Dewitt, R.S. (2002, December). Crohn’s disease. Gale Encyclopedia of Medicine.

National Digestive Diseases Information Clearinghouse (NDDIC). (2003, January). Crohn’s disease [NIH Publication No. 03-3410].

National Library of Medicine. (nd). Crohn’s disease. MedlinePlus Tutorial.

 Posted on : May 17, 2014