Refractory Celiac Disease: When Healing Stalls

You’ve been strictly gluten-free for a year. Maybe two. But you’re still sick. Your antibodies haven’t normalized. Your symptoms persist. Your biopsy still shows damage.

This isn’t supposed to happen. What’s going on?

When the Diet Should Work

For most celiacs, the timeline looks like:

• Symptoms improve within weeks to months
• Antibody levels drop over 6-12 months
• Intestinal healing (verified by biopsy) by 12-24 months

If you’re beyond this timeline and not improving despite strict adherence, something else is going on.

Possible Explanations

Hidden Gluten Exposure

The most common reason for persistent symptoms or elevated antibodies: you’re still getting glutened.

Sources to investigate:

• Cross-contamination at home
• Eating out more often than you realize
• Hidden gluten in medications or supplements
• Communion wafers (if receiving)
• Cosmetics and lip products
• A shared kitchen that isn’t safe
• Foods you assumed were safe but aren’t

What to do: Work with a celiac-savvy dietitian to audit your diet. They often find sources patients missed.

Other Food Intolerances

Damaged intestines may react to other foods:

• Lactose intolerance: Common, often temporary during healing
• Fructose malabsorption: Some celiacs develop this
• Other intolerances: Eggs, soy, etc.

What to do: An elimination diet or breath testing can identify these.

Associated Conditions

Celiac disease is associated with other conditions:

• Microscopic colitis: Inflammation in the large intestine, causes diarrhea
• SIBO (Small Intestinal Bacterial Overgrowth): Bacteria in the small intestine causing symptoms
• Pancreatic insufficiency: Your pancreas may not be producing enough enzymes
• Other autoimmune diseases: Thyroid, diabetes, etc.

What to do: Work with your gastroenterologist to test for these.

True Refractory Celiac Disease

If hidden gluten and associated conditions are ruled out, you may have refractory celiac disease (RCD), celiac that doesn’t respond to the gluten-free diet.

This is rare. Only about 1-2% of celiac patients develop RCD.

Two Types

Type 1 RCD:

• Normal-appearing lymphocytes (immune cells)
• Better prognosis
• May respond to immunosuppressive medications
• Usually doesn’t progress

Type 2 RCD:

• Abnormal lymphocytes (with concerning cell markers)
• More serious
• Risk of progression to lymphoma
• Requires close monitoring and aggressive treatment

Type 2 is concerning because those abnormal cells can become cancerous. This is why proper diagnosis and follow-up matter.

Diagnosis

RCD is diagnosed when:

1. You’ve been strictly GF for at least 6-12 months
2. Other causes are excluded (hidden gluten, other conditions)
3. Biopsy shows persistent villous atrophy
4. Lymphocyte analysis distinguishes Type 1 from Type 2

This requires a specialist, ideally at a celiac center.

Treatment for RCD

Type 1 RCD

• Confirm absolute gluten elimination
• Possible steroid treatment (budesonide, prednisone)
• Nutritional support (IV nutrition in severe cases)
• Monitoring for progression

Many Type 1 RCD patients stabilize or improve with treatment.

Type 2 RCD

• Aggressive treatment (chemotherapy-like agents in some cases)
• Close monitoring for lymphoma development
• Management at a specialized center
• Nutritional support

Type 2 is serious and requires expert care.

What to Do If You’re Not Healing

Step 1: Get Expert Help

If you haven’t seen a celiac specialist, now is the time. University celiac centers have more experience with complex cases.

Step 2: Diet Audit

Before assuming you have RCD, eliminate hidden gluten sources with a dietitian’s help.

Step 3: Test for Other Conditions

Rule out associated conditions that might explain symptoms.

Step 4: Repeat Testing

If your initial blood work and biopsy are old, repeat them after confirmed strict adherence.

Step 5: Specialized Testing

If all else fails, referral for lymphocyte analysis and consideration of RCD.

Questions to Ask Your Doctor

• “Could there be hidden gluten exposure we haven’t identified?”
• “Should we test for associated conditions like SIBO or microscopic colitis?”
• “Are my current antibody levels and biopsy consistent with ongoing damage?”
• “Do you have experience with refractory celiac, or should I see a specialist?”
• “What would distinguish Type 1 from Type 2 RCD in my case?”

The Emotional Weight

Being stuck in ongoing symptoms despite doing everything right is exhausting and demoralizing.

You might feel:

• Like you’re doing something wrong
• Frustrated with doctors who can’t help
• Afraid of what ongoing damage means
• Isolated because “just follow the diet” doesn’t work for you

These feelings are valid. Seek support, from celiac communities, from a therapist who understands chronic illness, from anyone who gets it.

Most People Aren’t Refractory

Here’s the reassuring news: most people who aren’t healing have hidden gluten exposure or an associated condition. True RCD is uncommon.

So before you spiral into fear about refractory disease:

1. Get expert help
2. Audit your diet thoroughly
3. Test for other conditions
4. Then, if necessary, pursue RCD evaluation

The odds are in your favor. But if you do have RCD, you need to know, because treatment exists, and early intervention matters.

A Note on Hope

Even refractory celiac disease isn’t hopeless. Type 1 often responds to treatment. Type 2 is more serious but manageable at specialized centers.

Research continues. Clinical trials exist. The medical community is paying more attention to refractory disease than ever before.

If this is your diagnosis, you’re not abandoned. Care exists. Keep advocating for yourself.