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How do you diagnose Crohn's disease?

There is no single test to establish the diagnosis of Crohn's disease. The diagnosis of Crohn's disease is made using a combination of modalities:

  • Clinical history
  • Physical examination
  • Laboratory tests
  • Endoscopy (Gastroscopy/Colonoscopy)
  • X-ray findings (small bowel series, computed tomography (CT scan), magnetic resonance imaging (MRI)
  • Tissue biopsy (pathology)

History and Physical Exam

There is no substitute for a good history and physical exam. The patient will be asked a number of questions regarding your symptoms to narrow down the possible diagnoses. The details of your medical history help us decide what testing is necessary. The patient will be asked about the chronicity (length of time), acuity, and severity of the symptoms. You will be asked questions regarding palliative (things that ease symptoms) and provocative (things that make symptoms worse) factors, particularly whether food or bowel movements improve or worsen the symptoms. Recent antibiotic or NSAID use, sick contacts, travel, smoking history and family history of GI disorders are all important clues.

The physical exam is also critical in making a definitive diagnosis. The patient will be assessed for mouth ulcers, abdominal discomfort when pressing on the abdomen, masses in the abdomen, rashes, joint swelling and perianal disease (sores in your rectum or perineum).

Blood Tests

There are a number of blood tests that may be helpful in making the diagnosis of Crohn's disease. A compete blood count (CBC) may show anemia (low red blood cells), or may demonstrate an elevated white blood cell (WBC) or platelet count (PLT), the latter of which are both markers of inflammation or infection. Sedimentation rate (ESR) and C-reactive protein (CRP) are other non-specific markers of inflammation that are often measured during the work-up of Crohn's disease. Low albumin (blood protein) can also be seen in patients with long-standing or severe symptoms. These tests can confirm that there is ongoing inflammation, but do not diagnose specifically what is causing the inflammation. The stool can also be tested for bacteria and parasites, both of which can cause infections that can mimic the symptoms of Crohn's disease. There are some newer stool tests available that test for the presence of intestinal inflammation, but like the serum (blood) tests these are not specific for Crohn's disease and can be seen with other intestinal diseases and infections.

The CBC, ESR, and CRP are blood tests that are often followed serially in patients with well established Crohn's disease to assess for inflammation, particularly when a patient is complaining of symptoms that may indicate a flare of their disease. If a patient having symptoms gives a history of recent international travel, consumption of undercooked or raw foods, or recent antibiotics use for an unrelated illness, stool studies to assess for the presence of bacteria or parasites may be checked to ensure that there is not an accompanying GI infection.

There are a number of newer serologic markers (ASCA, ANCA, ompC, anti-CBir1) that may assist in making the diagnosis of Crohn's disease. As of yet, these markers still are not accurate enough to make a diagnosis of Crohn's disease on their own. However, they may be helpful if used in combination with the history, physical exam, radiologic, and endoscopic findings, and should be considered an adjunct to conventional testing.


Very often, inspection of the lining of the intestines with colonoscopy, sigmoidoscopy, or  endoscopy using a fiberoptic endoscope is necessary to help establish the diagnosis of Crohn's disease. A long, flexible tube with a light source and an attached camera is inserted into the anus ("sigmoidoscopy" if only the lower third of the colon is examined, "colonoscopy" if the full colon is examined). A colonoscopy is often preferred when Crohn's disease is being considered because it is often possible to advance the scope into the end of the small intestine known as the terminal ileum, a common site for Crohn's disease involvement. In Crohn's disease, the lining of the colon and/or terminal ileum appears swollen, inflamed, with frequent ulcerations. The inflammation is often patchy and discontinuous,unlike ulcerative colitis.

Normal small bowel (left) and small bowel in Crohn's disease (right)
Normal colon (left) and Crohn's ulcer in colon (right)

Tiny samples, or biopsies, of the lining of the colon are taken during the procedure, so that a pathologist may examine them under the microscope to look for signs of inflammation. A specific type of inflammation known as non-caeseating granulomas can be seen in up to 20% of patients with Crohn's disease and is very helpful in confirming the diagnosis. The combination of endoscopy and pathology is almost always necessary to make the diagnosis of Crohn's disease. This procedure may be postponed in patients with signs of severe colitis, as the lining of the colon becomes very fragile and easy to damage with the endoscope.

Occasionally, if patients have many upper GI symptoms such as upper abdominal pain, reflux, and/or nausea, a gastroscopy or  upper endoscopy may be performed to examine the esophagus, the stomach, and the first part of the small bowel (duodenum).


CT scan of patient with narrowing (yellow arrow) of small bowel due to Crohn's disease

Because endoscopy and colonoscopy can only see the very beginning and end of the small intestine, there are a number of radiologic tests that are used to evaluate the small intestine. The test that has been most used to evaluate the small intestine is the small bowel series (also called upper GI series or small bowel follow through), In this test, a patient will drink barium and then undergo a series of x-rays that will demonstrate inflammation, fistulas or strictures of the small intestine, if present. More recently many gastroenterologists have been using, other radiologic tests such as  CT scans and  MRIs to provide a complete evaluation of the intestines, and to rule out complications of Crohn's disease such as perforations, abscesses, and fistulas. CT scans and MRIs mainly are used to look outside the bowel wall for complications of Crohn's disease, but new oral contrast dyes and specialized techniques (enterography) are enabling these tests to look closely at the walls of the small intestine as well.

Capsule Endoscopy

Capsule endoscopy is a novel imaging modality that permits the inspection of the small bowel. Patients will swallow a pill that contains a camera embedded inside. The camera then transmits pictures to a recording device and thereby permits inspection of most of the internal lining (mucosa) of the small bowel in a relatively non-invasive manner. It is mainly used for patients with GI bleeding when no source can be found on upper endoscopy and colonoscopy.

Care must be used in patients with known Crohn's disease due to the risk of capsule retention (capsule getting stuck in the intestine). A retained capsule will often require surgical removal. Additionally, these studies must be evaluated carefully to avoid misdiagnoses; for example, NSAIDS can cause ulcerations in the small intestines which may be mistaken for the similar-appearing lesions of Crohn's disease, and asymptomatic ulcerations can actually be seen in up to 15% of the general, otherwise healthy population. Currently, capsule endoscopy does not examine the esophagus, stomach or colon and does not take biopsies; therefore it is not a substitute for endoscopic procedures, but it may be useful in specific circumstances.

Contact Information

Inflammatory Bowel Disease Program
Digestive Disease Center
Beth Israel Deaconess Medical Center
330 Brookline Avenue
Boston, MA 02215