Crohn’s vs Celiac: How to Tell the Difference

Medically Reviewed by Minesh Khatri, MD on August 12, 2022
4 min read

It’s normal to have gut problems once in a while. But if you’re always in pain or running to the bathroom, you might have a digestive disorder like Crohn’s disease or celiac disease.

Celiac disease means your body can’t digest gluten, a protein in many grains like wheat, rye, and barley. If you do eat it, it makes your immune system attack your small intestine. Conditions that cause your immune cells to fight against your body are called autoimmune disorders.

Crohn’s disease, on the other hand, is an inflammatory bowel disease. It’s also an autoimmune condition, but doctors don’t know what causes it. It leads to inflammation -- swelling, redness, or tenderness -- in the lining of your digestive tract. It can also trigger inflammation in other areas of your body, like your eyes and joints.

It’s easy to confuse the two diseases. And some people have both at the same time. Here’s how to tell them apart.

Celiac disease and Crohn’s disease happen when your immune system doesn’t work normally. In both cases, that leads to inflammation in your intestines and sometimes other body parts, too. They can cause symptoms like:

Doctors don’t know exactly what causes either disease. But recent research shows that they’re genetically similar. Scientists have found four genes that make a person more likely to get celiac and Crohn’s.

Sores. Crohn’s can cause sores called pyoderma gangrenosum anywhere in your body, though they usually show up on your legs. You can get sores called abscesses around your bottom. Most of the sores Crohn’s causes are inside your body, in the lowest part of your small intestine and your colon.
Sometimes two sores merge and form a tunnel between them called a fistula.

Eyes. Only Crohn’s can cause inflammation in your eyes.

Treatments. You treat celiac disease by avoiding foods with gluten. But many people with Crohn’s can eat gluten with no problem. Instead, they might find it helpful to stay away from other foods, like dairy products or spicy foods. With Crohn’s, biologic medications can tone down inflammation in your body. Surgery also might help.

The best way to know what you have is to see your regular doctor or a gastroenterologist. To begin with, the process will be much the same:

  • The doctor will ask about your symptoms and family health history.
  • They may recommend blood tests. While not always accurate, they sometimes can show which condition you have.

If your doctor suspects celiac disease, they may do these tests:

  • Endoscopic biopsy: Your doctor will insert a thin tube through your mouth and into your gut to see inside your stomach and small intestines. Then, they'll take a small piece of tissue from the area and look at it under a microscope.

With Crohn’s, you may need these tests, among others, to diagnose the disease.

  • Colonoscopy: Your doctor will put a scope inside your bottom to look at your colon.
  • Upper endsoscopy: The doctor will slide a thin tube with a camera on it through your mouth to see inside your gut.
  • CT scan or MRI: These imaging tests provide a clear look at the structures inside your body.

Treatment for celiac disease is far more simple.

Gluten-free diet: This is the centerpiece of treatment for celiac disease. The doctor will tell you to start eating this way before you leave the office. Most people with celiac have to avoid these foods for the rest of their lives:

  • Wheat
  • Barley
  • Bulgur
  • Durum
  • Farina
  • Graham flour
  • Malt
  • Rye
  • Semolina
  • Spelt (a form of wheat)
  • Triticale

Once you stop eating gluten, the inflammation in your gut should get better. If your small intestine is severely damaged, you may need steroids.

Treatments for this condition are wide ranging and include a mix of medications, treatments, and surgery. Among the most common medications are:

Antibiotics: They help heal the sores Crohn’s can cause. They may even get rid of harmful bacteria in your intestines that kick-start Crohn’s inflammation. Commonly used ones include:

  • Ciproflaxin (Cipro)
  • Metronidazole (Flagyl)

Anti-inflammatory drugs: These drugs help ease inflammation. The two main types in use are:

  • Corticosteroids
  • Oral 5-aminosalicylates (5-ASA)

Immune system suppressants: They target the cause of inflammation within your immune system. You might get:

  • Adalimumab (Humira)
  • Azathioprine (Azasan, Imuran)
  • Certolixumab pegol (Cimzia)
  • Infliximab (Remicade)
  • Mercaptopurine (Purinethol, Purixan)
  • Methotrexate (Trexall)
  • Natalizumab (Tysabri)
  • Ustekinumab (Stelara)
  • Vedolizumab (Entyvio)

Over-the-counter medications: These can also play a role in treatment. You might take:

  • Antidiarrheal medicine
  • Pain relievers
  • Iron supplements
  • Calcium supplements
  • Vitamin D supplements

Nutrition therapy: Your doctor might prescribe a special liquid diet to replace nutrients and give your bowel a rest, especially if you’re getting ready for surgery. They might also combine it with medications. 

Low-residue or low-fiber diets can help you poop less. Your doctor might put you on one if you have a narrow place in your bowel called a stricture.

Surgery: This is an option if other treatments don’t help. The doctor removes the damaged section of your intestine and joints the healthy parts back together. The relief usually doesn’t last long -- the disease can affect the reconnected areas. So you’ll still need medications after the operation.