How Crohn’s Disease Affects the Digestive Tract

Many people have heard of Crohn’s disease, but they may not be familiar with what it means to a patient who has the disease. While Crohn’s disease may have some name recognition, it might still not be known that it is just one type of inflammatory bowel disease (IBD) and that ulcerative colitis is also a form of IBD. Crohn’s disease affects the digestion, and while for most people that means the intestines, Crohn’s disease can affect other parts of the body as well. Here are some of the body parts that Crohn’s disease can affect.​


Small and Large Intestine

Large And Small Intestine

GYRO PHOTOGRAPHY/amanaimagesRF/Getty Images

The small and large intestines are the most common places for Crohn’s disease to cause inflammation. Many people may mistakenly believe that it is only the small intestine that is affected. But the large intestine is also commonly affected in Crohn’s disease, and about 20% of people have the disease only in the large intestine (which is called Crohn’s colitis).

The most common form of Crohn’s, which affects about 50% of patients, is called ileocolitis and does affect the last section of the small intestine (the ileum) and the large intestine. The second most common form, ileitis, affects about 30% of patients and affects the ileum. The classifications are mostly for the benefit of a treatment plan, and the type of Crohn’s disease a patient has can change if other parts of the intestine become affected. 


The Mouth

Mouth Exam

BSIP/UIG/Getty Images

One problem that many with IBD experience are aphthous stomatitis, which are ulcers in the mouth. It’s estimated that 20% to 30% of people with Crohn’s disease have this problem. The ulcers tend to occur when the Crohn’s disease is active, but they can also occur during times of remission as well.

People with Crohn’s disease may also experience other various problems in the mouth, such as inflammation in the lips or on the tongue. Sometimes problems in the mouth could be due to vitamin deficiencies, which are common in people with IBD. If there is a lot of vomiting, the enamel of the teeth could wear down, causing dental problems. People with IBD also tend to need more dental work in general and may be prone to infection in the gums.


The Esophagus

Gastroscopy, Ilustration
Getty Images/BSIP/UIG

Crohn’s disease in the esophagus is rare, affecting less than 1% of Crohn’s patients. When the esophagus does become affected by Crohn’s disease, it can lead to problems with swallowing and cause heartburn. If this type of Crohn’s disease is suspected, tests such as an upper endoscopy might be done to look for inflammation or other complications such as strictures or fistulas.


The Stomach


MediaForMedical/UIG/Getty Images

In about 5% of patients with Crohn’s disease, the stomach may be affected. The two forms that affect the stomach are called jejunoileitis and gastroduodenal Crohn’s disease. In jejunoileitis, the middle part of the small intestine, which is called the jejunum. is also affected. In gastroduodenal Crohn’s disease, the first part of the small intestine, the duodenum, is also inflamed. In some cases, these forms of Crohn’s disease may initially be thought to be a stomach ulcer, but as the symptoms continue, it is discovered later that it is actually Crohn’s disease.


Perianal Area

A woman with a hurting butt region

 ChesiireCat/Getty Images

The perianal area is the skin and the area around the anus. Crohn’s disease affecting the perianal area is quite common. Some of the problems that can occur include perianal abscesses, fistulas, anal fissures, and hemorrhoids. An abscess is a collection of blood and pus, and as many as 62% of people with Crohn’s disease may develop one during the course of their disease.

Abscesses may lead to the development of a fistula, which is an abnormal connection between two organs or between the interior of the body and the skin. There are conflicting estimates of the prevalence of anal fissure—a small tear in the anal canal—in people with Crohn’s disease, varying from about a third to more than half of patients. Hemorrhoids, while common in the general population, are not as much of a concern in people who have Crohn’s disease.

The Importance of Managing Crohn’s Disease

Crohn’s disease can affect any part of the digestive system, with the large and small intestine are the most common locations. However, inflammation can happen in other locations as well, and in fact, this may be fairly common. When new signs and symptoms occur, people with Crohn’s disease should keep in close contact with their gastroenterologist to manage their disease.

6 Sources
Verywell Health uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read our editorial process to learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.
  1. Feuerstein JD, Cheifetz AS. Crohn disease: epidemiology, diagnosis, and management. Mayo Clin Proc. 2017;92(7):1088-1103. doi:10.1016/j.mayocp.2017.04.010

  2. Lankarani KB, Sivandzadeh GR, Hassanpour S. Oral manifestation in inflammatory bowel disease: a review. World J Gastroenterol. 2013;19(46):8571–8579. doi:10.3748/wjg.v19.i46.8571

  3. Schwartzberg DM, Brandstetter S, Grucela AL. Crohn's disease of the esophagus, duodenum, and stomach. Clin Colon Rectal Surg. 2019;32(4):231-242. doi:10.1055/s-0039-1683850

  4. Crohn’s & Colitis Foundation. Overview of Crohn’s disease.

  5. Sordo-Mejia R, Gaertner WB. Multidisciplinary and evidence-based management of fistulizing perianal Crohn’s disease. World J Gastrointest Pathophysiol. 2014;5(3):239-251. doi:10.4291/wjgp.v5.i3.239

  6. D’Ugo S, Franceschilli L, Cadeddu F, et al. Medical and surgical treatment of haemorrhoids and anal fissure in Crohn’s disease: a critical appraisal. BMC Gastroenterol. 2013;13(1):47. doi:10.1186/1471-230X-13-47

By Amber J. Tresca
Amber J. Tresca is a freelance writer and speaker who covers digestive conditions, including IBD. She was diagnosed with ulcerative colitis at age 16.