How Crohn's Disease Is Diagnosed

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Diagnosing Crohn’s disease can take time and careful consideration for several reasons. This form of inflammatory bowel disease (IBD) has symptoms similar to other conditions, which can make diagnosis problematic. In addition, distinguishing Crohn’s disease from ulcerative colitis (and vice versa) can also be challenging.

Receiving an accurate diagnosis of Crohn’s disease and starting treatment right away is important to avoid complications from the progression of the disease. There may be several tests that are used to help diagnose Crohn’s disease and to pinpoint the location(s) of any inflammation.

Crohn's disease diagnosis
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There are several types of imaging tests used to diagnose Crohn's disease.


A colonoscopy allows a look inside the large intestine (colon). During this test, a physician may see the characteristics of Crohn’s disease inside the large intestine. This can include inflamed areas or ulcers that may occur in patches. Inflammation in the lining of the colon may look red and swollen and ulcers may look like rows or tracts. There can be diseased tissue and healthy tissue alternating in different areas of the colon.

A colonoscope is a long, thin, flexible tube with a camera and a light on the end. This tool is passed through the anus and into the large intestine in order to get a close look at the lining of the organ and take biopsies. Patients prepare for this test by clearing their large intestine of stool. Every physician will have slightly different instructions on how to do this, but in most cases, it involves fasting the day or night before the test and using a combination of strong laxatives to clear out the stool.

It’s important to follow instructions closely to ensure the test goes as well as possible and that the physician can get a clear, unobstructed view of the colon wall.

Crohn's Disease Doctor Discussion Guide

Get our printable guide for your next doctor's appointment to help you ask the right questions.

Patients are sedated during a colonoscopy so there isn’t any pain or discomfort. An IV will be started to give the sedating medications. The sedation will be stopped after the test, but because the medications used will cause grogginess, patients must be driven home by a friend or a relative after the test.

Small pieces of tissue (biopsies) will be taken during a colonoscopy so that the cells from both the inflamed areas and the healthy areas can be examined more closely and tested in a lab. The results of these biopsies can help in making the diagnosis.

After the colonoscopy is over, patients are monitored for a little while and given instructions and any restrictions for the rest of the day. Most people can return to their regular activities the day after the test.

Upper Endoscopy

An upper GI endoscopy and enteroscopy is a test that is done to look inside the esophagus, stomach, and duodenum. Because Crohn’s disease can affect the upper digestive tract as well as the lower, this test might be used to look for any patches of disease in these organs.

A tool called a fiberoptic endoscope that has a light and a camera is inserted through the mouth and down through the esophagus, stomach, and into the first section of the small intestine. Biopsies will be taken in order to look at the tissue more closely and observe any signs of Crohn’s disease.

Preparation for an upper endoscopy involves fasting for several hours before the test so that the stomach is empty of any food. The test is done with the use of sedation in order to minimize discomfort, but patients are awake during the test in order to be able to respond to instructions. This means, however, that patients will need someone to take them home after the test.

The throat is numbed during the procedure, but the effect should wear off soon after the test is completed. If there are any results to report, the physician might be able to talk about them after the test, but there may also be a need for a follow-up to discuss next steps.

In some cases, the physician completing the test may be able to give some insight as to what was found (if anything) during the test, and there may also be a follow-up scheduled to go over any results more carefully. If there’s a diagnosis of Crohn’s disease, there will also be a need for a treatment plan to be put in place.

Computed Tomography Enterography (CTE) Scan

A CT scan is a type of X-ray that’s used to see internal tissues and organs. The images provided by this test offer a cross-sectional view of the abdomen and pelvis, and is specifically designed to identify and locate problems within the bowel, such as inflammation, bleeding, obstructions, and any other signs of Crohn's disease. A CT enterography (CTE) measures the thickness of the bowel, as well.

A magnetic resonance enterography (MRE) is able to produce even more detailed pictures than a CTE, further differentiating between old and new inflammation, plus showing strictures or narrowing or signs of fibrosis.

The CT scanner is a machine that has a round opening in the middle. Patients lie on a table that slides into the opening of the scanner during the test. It will be necessary to stay still during the test, as the machine rotates around and takes the images. At times, a technician will also give instructions to hold the breath for a few seconds at certain times.

Patients are asked to fast about four hours prior to the test, drinking only water. Contrast is given during a CT scan, which helps with the visualization of the organs. The contrast may be given as a drink, in an IV, or as an enema.

For oral contrast, patients are given a drink containing barium to swallow, which is often easier to do if it’s been chilled and while using a straw. During the test, contrast dye will also be given through an IV. Lastly, if necessary, an enema containing barium may be given. All these types of contrast will help in visualizing the digestive organs and in helping physicians make a diagnosis.

Capsule Endoscopy

A capsule endoscopy is done by swallowing a camera that is the size of a pill. This procedure is usually performed only after a CTE or MRE, as it's necessary to first check for small bowel disease strictures or narrowing—just to make sure the capsule doesn't get stuck.

The preparation for this test includes fasting for several hours beforehand. After the pill is swallowed, patients will wear a monitoring device that will capture the images sent from the camera in the pill as it travels through the small intestine. The camera will take photos all through the small intestine to give physicians a good look at the lining.

Patients will go about their normal activities during the day. The camera will pass through the entire digestive system and will leave the body through the anus during a bowel movement. It’s not necessary to retrieve the camera from the toilet, it can be flushed.

The device that’s worn to capture the images will need to be returned to the physician’s office in order to retrieve the images. A follow-up appointment may be made in order to discuss any findings on the photos and if treatment is needed.

Labs and Tests

Blood tests won’t be used solely to diagnose Crohn’s disease but may be helpful in understanding how the disease has affected the body.

Two blood tests that may be ordered include the red blood cell and white blood cell counts. These tests will give information on the effects any blood loss and inflammation are causing. Other blood tests, including C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR), are used to measure inflammation in the body.

Liver function tests, an electrolyte panel, and a vitamin B12 level may also be done because while they’re not diagnostic, they can provide clues to how the IBD is causing effects outside the digestive system.

Stool Tests

Stool tests might be used to look for blood and also to rule out other potential conditions that could be causing symptoms. These tests won’t be used to diagnose Crohn’s disease alone. Stool collection is done either at home or at a lab, where the stool is placed into a sterile container and sent for testing.

Some of the potential findings could include bacteria, blood, or parasites. Bacterial infections are not uncommon in people with IBD, so it might be necessary to rule one out or to confirm it.

A very important stool test in the diagnosis and management of Crohn's disease is a fecal calprotectin test. This test examines stool samples for calprotectin, a protein found in white blood cells that signifies inflammation is likely present in the digestive tract and the body's white blood cells have been activated as a defense mechanism.

Differential Diagnoses

Some of the common symptoms of Crohn’s disease, such as abdominal pain and diarrhea, might be caused by other conditions, making it important to rule them out before diagnosing IBD.

  • Bacterial colitis: Colitis, which is inflammation in the colon, can also be caused by a bacterial infection such as from E. coli.
  • Clostridioides difficile (C. diff) infection: A bacterial infection with C. diff may cause symptoms of diarrhea and pain, which is why it might need to be ruled out with a stool test.
  • Ischemic colitis: This type of colitis is caused by a lack of blood flow to the colon and needs treatment immediately to prevent complications.
  • Microscopic colitis: In cases of continuing diarrhea, this type of colitis might need to be ruled out.
  • Parasitic infection: Parasites in the digestive system may also cause pain and blood in the stool, and these infections may be considered in those who have traveled to areas of the world where they are more common.
  • Ulcerative colitis: Ulcerative colitis and Crohn’s disease are both forms of IBD, but the treatments might be different, which is why a distinction is made between the two diseases.
  • Viral infection: Pain, vomiting, and diarrhea from viral gastroenteritis (the “stomach flu”) will usually resolve in a few days.

Frequently Asked Questions

  • Can a blood test detect Crohn’s disease?

    No. A blood test alone can't diagnose Crohn’s disease, but it can provide important information about your overall health and the impact the disease has had on your body so your symptoms can be properly treated.

  • Why is it so hard to diagnose Crohn’s disease?

    The most common symptoms of Crohn’s, including diarrhea, weight loss, and abdominal pain, can be mistaken for many other disorders. Further complicating the process is the fact that there is no single definitive test that allows doctors to diagnose Crohn’s disease.

3 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. National Institute of Diabetes and Digestive and Kidney Diseases. Diagnosis of Crohn’s disease

  2. Gecse KB, Vermeire S. Differential diagnosis of inflammatory bowel disease: imitations and complications. Lancet Gastroenterol Hepatol. 2018;3(9):644-653.

  3. Ha F, Khalil H. Crohn’s disease: a clinical update. Therap Adv Gastroenterol. 2015;8(6):352-359. doi:10.1177/2F1756283X15592585

Additional Reading
  • Crohn’s and Colitis Foundation. Diagnosing Crohn's Disease and Ulcerative Colitis. 31 May 2010.  

  • The National Institute of Diabetes and Digestive and Kidney Diseases. Diagnosis of Crohn’s Disease. National Institutes of Health. Sept 2017.

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.