CT Enterography vs MRE in Crohn’s: Why Your GI Chooses One
Last Updated Jan 15, 2026
Crohn’s disease can affect the full thickness of the bowel wall and areas outside the bowel, not only the inner lining seen on colonoscopy. That is why a gastroenterologist may order cross-sectional “enterography” imaging to look at the small intestine and nearby tissues. Two common options are computed tomography (CT) enterography and magnetic resonance (MR) enterography. They can feel similar from a patient point of view, but the choice is often based on safety (especially radiation), how fast results are needed, and what complication the care team is trying to rule in or rule out.
What CT enterography (CTE) and MR enterography (MRE) have in common
Both CT enterography (CTE) and MR enterography (MRE) are designed to make the small bowel easier to see. In both tests, patients typically drink a large amount of liquid contrast to “fill and stretch” the small intestine so inflammation, narrowing (strictures), and other changes are easier to spot. CT enterography is a CT scan that uses this special oral contrast to get a better view of the intestines. [1]
These tests are often used to map where Crohn’s disease is active and to look for complications. CT enterography, for example, is commonly used to identify small bowel inflammation, bleeding sources, obstruction, and Crohn’s-related complications such as abscesses and fistulas, and it can help visualize the bowel wall beyond just the inner surface. [2]
From a guideline perspective, multiple imaging options can be reasonable in Crohn’s, depending on the situation. The American College of Radiology (ACR) Appropriateness Criteria list both MR enterography and CT enterography as “usually appropriate” options across common scenarios such as suspected Crohn’s disease, suspected flare in known Crohn’s, and imaging for surveillance or monitoring therapy. [3]
Why a gastroenterologist might choose one over the other
Radiation concerns often push the decision toward MRE when time allows. CT uses ionizing radiation, while MR does not. RadiologyInfo (from the American College of Radiology and the Radiological Society of North America) notes that MR enterography does not use ionizing radiation and may be preferred for younger people with inflammatory bowel disease who may need multiple exams over their lifetime. The same source also notes a practical difference: MR enterography usually takes longer (about 30 to 45 minutes) than CT enterography (about two to four minutes). [4]
Speed and urgency may push the decision toward CTE. When symptoms are severe, when there is concern for a complication, or when rapid imaging is needed, a faster scan can matter. Shorter scan time can also help when staying still or holding breath is difficult.
Accuracy is similar overall, but the “best” test depends on the question. A meta-analysis comparing MRE and CTE for small bowel Crohn’s disease found that their overall diagnostic performance for active disease is comparable, supporting MRE as a radiation-free alternative in many situations. [5]
Contrast type and medical history can influence the choice. CT commonly uses iodine-based intravenous contrast, while MR often uses gadolinium-based contrast. The U.S. Food and Drug Administration has warned that gadolinium-based contrast agents can rarely be linked to nephrogenic systemic fibrosis in certain patients with severe kidney dysfunction, so imaging teams may screen for kidney problems when contrast is planned. [6]
When deciding between CTE vs MRE, many people find it helpful to ask the care team what clinical question the scan is meant to answer (inflammation, stricture, fistula, abscess, obstruction, or treatment response) and how radiation exposure, scan time, and contrast safety fit into that specific situation.