Mucosal Healing in Crohn's Disease: What It Is and Why It Matters
Published on May 1, 2026
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Crohn’s disease, a chronic inflammatory bowel disease (IBD), damages the lining of your gastrointestinal (GI) tract and causes symptoms like abdominal pain, fatigue, and diarrhea. In the past, treatment focused on managing symptoms. But this goal has changed, and treatment plans now work toward what’s known as mucosal healing.
Your intestinal mucosa, the layer of cells that line your GI tract, protects your intestines from bacteria and other harmful substances. But Crohn’s inflammation can damage that lining, which causes symptoms and increases your risk of infection. Because of this, mucosal healing has become a more common Crohn’s treatment goal.
“We’re no longer aiming solely for symptom control; we’re aiming for deeper healing and better long-term outcomes,” says Joseph Sleiman, MD, a gastroenterologist at Cleveland Clinic. “That often means monitoring the disease more proactively and adjusting treatment even when patients feel well, with the goal of preventing complications before they develop.”
What Does Mucosal Healing Mean?
Mucosal healing generally means that your intestinal lining has no visible inflammation or damage, but not all experts agree on this definition. Your provider can see this result by looking at the inside of your intestines with a camera on a thin tube inserted through the anus or mouth during either a colonoscopy or endoscopy procedure.
Some providers define mucosal healing using the STRIDE-II (selecting therapeutic targets in inflammatory bowel disease) guidelines, which give a score based on whether you have visible inflammation or damage, says Jill Gaidos, MD, a gastroenterologist and the director of clinical research at the Yale Inflammatory Bowel Disease Program in New Haven, Connecticut. “This is the definition of mucosal healing that I use in my clinical practice,” she says.
Other providers may use different scoring systems to confirm healing by looking at the GI tract directly during an endoscopy or colonoscopy.
Your doctor may also perform a biopsy by removing intestinal tissue during this examination. A pathologist will then look at the sample under a microscope to check for signs of mucosal healing that may be invisible to the naked eye.
Once your mucosal lining heals, your provider may order regular stool and blood tests to make sure that your inflammation hasn’t come back. If it returns, they can then adjust your treatment early on.
Why Mucosal Healing Matters for Managing Crohn’s Disease
Mucosal healing plays an important role in long-term Crohn’s management — even more than symptom relief. “One of the challenges in Crohn’s disease is that symptoms don’t always reflect what’s happening internally,” says Dr. Sleiman. That means that even if you feel pretty good, your intestine may still have damaging inflammation.
“When we focus on long-term healing, specifically healing of the intestinal lining, we see better outcomes, including lower rates of treatment failure, fewer hospitalizations, and a lower likelihood of surgery,” says Sleiman.
When you target symptoms alone, ongoing inflammation can still increase your risk for complications, says Dr. Gaidos. Possible complications include the following:
- Bowel Obstruction When fluid, stool, and air can’t move through your intestine, it leads to a backup.
- Fistulas These abnormal openings can form between organs or from an organ through your skin.
- Abscesses These infected, painful areas are filled with pus.
- Fissures Small, painful cracks in your anus can itch and bleed.
- Ulcers This includes open sores anywhere in your GI tract, like your mouth or perineum (the area between your anus and genitals).
But when your mucosal lining heals, even beyond when the symptoms have gone away, you can lessen long-term damage and prevent complications. “It’s about treating the underlying disease process rather than managing how someone feels in the moment,” says Sleiman.
How to Achieve Mucosal Healing in Crohn’s Disease
You can work toward mucosal healing in Crohn’s with medical treatment supported by a gut-healthy diet.
Medications for Mucosal Healing
Older medications like 5-aminosalicylates (5-ASAs) and corticosteroids (steroids) are sometimes prescribed for Crohn’s to calm the immune system and decrease inflammation. But the American College of Gastroenterology no longer recommends 5-ASAs for Crohn’s, and steroids are used only in the short term to begin the healing process, until a medication that’s suitable for long-term use can be started.
The most promising treatments for mucosal healing are advanced therapies like biologics and targeted oral medications, which manage your immune response more precisely, says Sleiman. “These therapies have significantly improved our ability to control inflammation at its source,” he says.
The treatments that have the best results are anti-TNF agents and JAK inhibitors, says Sleiman, adding that these advanced therapies that are approved by the U.S. Food and Drug Administration (FDA) are a great option for mucosal healing.
Anti-TNF medications that block an inflammatory protein called tumor necrosis factor alpha are used to promote mucosal healing:
- vedolizumab (Entyvio)
- ustekinumab (Stelara)
- infliximab (Remicade)
JAK inhibitors block inflammation-causing enzymes called janus kinases. Although the best ones for Crohn’s are still being studied, the current options include the following:
- filgotinib (Jyseleca)
- upadacitinib (Rinvoq)
Experts are also researching a biologic medication category called IL-23 inhibitors, which block a specific kind of cytokine, a protein that causes inflammation:
- risankizumab-rzaa (Skyrizi)
- guselkumab (Tremfya)
- mirikizumab-mrkz (Omvoh)
Your provider will recommend medications based on the Crohn’s severity and how high your risk is for complications, says Gaidos. “For those higher-risk patients, treatment with an advanced therapy is recommended,” says Gaidos.
Crohn’s Diet and Its Supportive Role
Diet can support your overall health and help you manage Crohn’s symptoms, but it can’t lead to mucosal healing on its own, says Sleiman.
Research shows a strong connection between dietary treatments and Crohn’s improvement in children, but experts haven’t seen it work as well in adults, says Gaidos. “There is an upcoming study that will hopefully provide more information on the role of diet with medications in adults with Crohn’s disease.”
However, working with a dietitian who specializes in IBD is very helpful, as diets need to be adjusted depending on the nutritional needs at various stages of healing, says Gaidos.
These diets promote healing in Crohn’s:
Your dietary plan will depend on your recommended diet and individual food restrictions. But these diets typically encourage increased consumption of fruits, vegetables, and lean proteins, and avoiding most dairy products, tea, coffee, alcohol, and canned foods.
Fecal Microbiota Transplantation
Researchers are studying fecal microbiota transplantation (FMT) to promote mucosal healing in Crohn’s, though limited research has shown conflicting results. FMT involves transplanting healthy donor stool into your colon to boost beneficial bacteria growth there. FMT can be done using endoscopy, colonoscopy, enema, or capsules taken orally, though it isn’t widely available because it’s still considered an experimental therapy with known and unknown risks.
Resources We Trust
- Mayo Clinic: Beyond Symptom Relief: Why Mucosal Healing Matters in Crohn’s Disease
- Cleveland Clinic: Crohn's Disease
- Gastrointestinal Society and the Canadian Society of Intestinal Research: Mucosal Healing in IBD (Crohn’s and Colitis) Video
- Guts UK: Crohn’s Disease
- Crohn's & Colitis Foundation: Bridging the Gap: Patient and Medical Perspectives on IBD Remission
EDITORIAL SOURCES
Everyday Health follows strict sourcing guidelines to ensure the accuracy of its content, outlined in our editorial policy. We use only trustworthy sources, including peer-reviewed studies, board-certified medical experts, patients with lived experience, and information from top institutions.
Resources
- Sands BE et al. Mucosal and Transmural Healing and Long-term Outcomes in Crohn’s Disease. Inflammatory Bowel Diseases. March 2025.
- Wang M et al. Emerging Strategy Towards Mucosal Healing in Inflammatory Bowel Disease: What the Future Holds? Frontiers in Immunology. December 13, 2023.
- Beyond Symptom Relief: Why Mucosal Healing Matters in Crohn’s Disease. Mayo Clinic. March 6, 2026.
- O'Moráin N et al. Mucosal Healing in Crohn's Disease: Bull's Eye or Bust? “The Pro Position”. Inflammatory Intestinal Diseases. November 3, 2021.
- Turner D et al. STRIDE-II: An Update on the Selecting Therapeutic Targets in Inflammatory Bowel Disease (STRIDE) Initiative of the International Organization for the Study of IBD (IOIBD): Determining Therapeutic Goals for Treat-to-Target strategies in IBD. Gastroenterology. April 2021.
- Definition & Facts for Crohn’s Disease. National Institute of Diabetes and Digestive and Kidney Diseases. July 2024.
- Lichtenstein GR et al. ACG Clinical Guideline: Management of Crohn’s Disease in Adults. The American Journal of Gastroenterology. June 2025.
- Xu M et al. JAK Inhibitor and Crohn’s Disease. Biomedicines. May 29, 2025.
- Partial Enteral Nutrition as Therapeutic Augmentation of Advanced Pharmacological Therapy in Patients With Active Crohn's Disease (PANDORA). ClinicalTrials.gov. February 25, 2026.
- Fecal Microbiota Transplant (FMT). Crohn’s and Colitis Canada.
- Fecal Transplant. Cleveland Clinic. August 21, 2023.
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