A colonoscopy is one of the most important tests doctors use to diagnose Crohn’s disease. It can help them detect signs of Crohn’s, like ulcers, fistulas, or skip lesions.

Crohn’s disease is an inflammatory condition that affects your gastrointestinal tract, most often the intestines (bowels).

To diagnose Crohn’s disease, doctors may perform a colonoscopy, which allows them to get a detailed look inside your bowels. A colonoscopy can provide essential information about the health of your intestines and reveal signs that can confirm a Crohn’s diagnosis.

In this article, we discuss what doctors look for during a colonoscopy for Crohn’s disease and other tests used to diagnose this condition.

A colonoscopy is a procedure that allows doctors to examine your intestinal lining using a flexible tube with a camera (a colonoscope). It enables them to view your:

  • ileum (last part of the small intestine)
  • entire large intestine (colon)
  • rectum

Colonoscopies provide clear images of your bowels, allowing doctors to detect signs of inflammation or damage that may indicate Crohn’s disease. An early diagnosis can help guide treatment and manage the symptoms.

During a colonoscopy, doctors look for specific signs in the colon that may suggest Crohn’s disease, including:


Ulcerations are sores or open wounds that can form in the lining of the colon. Colonoscopies can help doctors detect several kinds of ulcers, including:

  • Aphthous ulcers: These small, shallow ulcers usually look like white spots on the colonoscopy and can appear in the early stages of the disease.
  • Longitudinal ulcers: As Crohn’s progresses, tiny aphthous ulcers can group and merge, forming longitudinal ulcers. They can be round or irregular in shape and often have gaps.
  • Circumferential ulcers: These are deep ulcers that can affect the entire thickness of an intestinal wall.
  • Cobblestones: As Crohn’s progresses further, ulcerations can cover the entire intestinal wall, creating a characteristic cobblestone pattern. Cobblestones give the intestinal wall a bumpy look, resembling the surface of a cobblestone street.

Strictures and bowel obstruction

Over time, Crohn’s disease can thicken and scar the wall of your colon. This can cause your bowels to narrow (stricture) and potentially close up, leading to a bowel obstruction.

More than half of people with Crohn’s disease will develop a stricture in their lifetime.

Skip lesions

Skip lesions are patches of healthy tissue on the intestinal walls separated by areas of inflammation. This pattern is typical in Crohn’s and less so in ulcerative colitis (UC), another type of inflammatory bowel disease, making it a useful colonoscopy finding.


Pseudopolyps are small, raised bumps on the intestinal wall. As their name suggests, they are not true polyps (irregular growths), but scar tissue that has developed because of healing from inflammation. Pseudopolyps are common in both Crohn’s disease and UC.


Fistulas (or fistulae) are connections or tunnels that can form between the digestive tract and other organs or skin. For example, a fistula may form between the colon and bladder. This happens as ulcers deepen and extend through the entire thickness of the intestinal wall.

When you undergo a colonoscopy for Crohn’s disease, a healthcare professional will sedate you to help you relax and stay comfortable during the procedure.

Once you are sedated, the doctor will insert the colonoscope through your anus and carefully navigate it through your colon. The camera on the colonoscope will transmit live images to a monitor, allowing the doctor to examine the lining of your colon for signs of Crohn’s disease.

During the procedure, the doctor may take small samples from areas that appear unhealthy (a biopsy). These samples can help confirm the diagnosis and rule out other conditions like cancer.

In addition to a colonoscopy, doctors may use other tests to diagnose Crohn’s and assess its severity, including:

  • Imaging tests: CT and MRI scans can provide detailed images of your intestines and other abdominal organs. These tests can help identify strictures, fistulas, and other signs of Crohn’s disease.
  • Blood tests: Blood tests can check for anemia, which may result from chronic blood loss from inflammation. They can sometimes help distinguish between Crohn’s and UC.
  • Stool tests: A calprotectin stool test can detect signs of inflammation in your intestines by measuring levels of the protein calprotectin.
  • Capsule endoscopy: This test involves swallowing a small capsule with a camera that takes images of your digestive tract as it passes through. It can provide a more comprehensive view of your small intestine, which is harder to examine than the colon.

Can colon cancer look like Crohn’s?

Colorectal cancer (CRC) can have similar symptoms to Crohn’s disease, such as abdominal pain and changes in bowel habits. Additionally, people with Crohn’s colitis (a type of Crohn’s that affects only the colon) have a higher risk of CRC than other people.

If you have Crohn’s disease, regular colonoscopy can help detect CRC early on.

Was this helpful?

A colonoscopy is an important tool for diagnosing Crohn’s disease and guiding treatment. By looking for specific signs of the condition, doctors can confirm the diagnosis and help manage the disease.

If you’re scheduled for a colonoscopy, it’s natural to feel anxious, but knowing what to expect can help you prepare for the procedure and get the care you need. Always discuss any concerns or questions with a healthcare professional.