Intestinal Damage and Healing: What's Actually Happening

When you have celiac disease and eat gluten, your immune system attacks your small intestine. But what does that actually mean? What’s happening at a cellular level? And how does healing work?

Understanding the biology helps you understand why the diet is so strict, and why healing takes patience.

The Healthy Small Intestine

Your small intestine is where nutrients are absorbed from food. The inner lining is covered with tiny finger-like projections called villi. These villi:

• Increase surface area dramatically (if laid flat, your small intestine lining would cover a tennis court)
• Contain cells that absorb nutrients
• Have even tinier projections called microvilli
• Are constantly renewing (cells turn over every 3-5 days)

Healthy villi mean efficient absorption. They’re why you can eat a meal and actually get nutrition from it.

What Gluten Does

When someone with celiac disease eats gluten:

The Immune Response

1. Gluten proteins (particularly gliadin) cross the intestinal barrier
2. An enzyme called tissue transglutaminase (tTG) modifies the gluten
3. Immune cells recognize modified gluten as a threat
4. Inflammatory response is triggered
5. The immune system attacks the intestinal lining

This isn’t like food poisoning where the enemy is external. Your immune system attacks your own tissue. That’s what makes it autoimmune.

Villous Atrophy

The immune attack damages the villi. They become:

• Flattened: From tall finger-like projections to short or flat
• Blunted: Tips eroded away
• Atrophied: Overall shrinkage and loss of structure

This is called “villous atrophy” and it’s what doctors look for on biopsy.

The Marsh Scale

Pathologists grade intestinal damage on the Marsh scale:

• Marsh 0: Normal
• Marsh 1: Increased intraepithelial lymphocytes (IELs) but normal villi
• Marsh 2: Increased IELs plus crypt hyperplasia
• Marsh 3a: Partial villous atrophy
• Marsh 3b: Subtotal villous atrophy
• Marsh 3c: Total villous atrophy

Most people diagnosed with celiac have Marsh 3a-3c. The villi are significantly damaged.

The Consequences of Damage

Without healthy villi:

Malabsorption: You can’t absorb nutrients properly. This causes:

• Iron deficiency anemia
• Calcium/vitamin D deficiency (leading to bone loss)
• B12 and folate deficiency
• Protein malabsorption
• Fat malabsorption (causing diarrhea and weight loss)

Leaky gut: Damaged intestinal barrier lets things through that shouldn’t:

• More immune reactions
• Inflammation throughout the body
• Potential contribution to other autoimmune conditions

Symptoms: GI issues, fatigue, brain fog, and more, all stemming from the inability to absorb what you eat.

How Healing Works

Remove gluten, and the immune attack stops. The intestine can heal.

The Timeline

This varies significantly by person, but generally:

First weeks: Immune inflammation begins to calm. You might feel better quickly, or not.

1-3 months: Intestinal cells are regenerating. Villi beginning to recover. Symptoms often improving.

6-12 months: Significant healing. Many people show substantial improvement on follow-up biopsy.

1-2 years: Most adults achieve substantial healing. Some may take longer.

Complete healing: Not everyone achieves perfectly normal villi. Studies show:

• About 34% of adults have mucosal recovery at 2 years
• About 66% at 5 years
• Some never achieve complete histological recovery despite strict diet

Factors Affecting Healing

Age: Children heal faster than adults. Younger adults heal faster than older.

Severity of initial damage: More damage may take longer to recover.

Adherence to diet: Even small exposures set back healing. Strict compliance matters.

Other health factors: Other conditions, medications, nutritional status all play roles.

Unknown factors: Some people heal quickly on the same diet where others heal slowly. Genetics, microbiome, and other factors we don’t fully understand.

Measuring Healing

Symptoms

Symptom improvement is encouraging but isn’t the same as intestinal healing. Some people feel better before they’re healed. Others don’t feel symptoms from ongoing damage.

Blood Tests

tTG-IgA and other antibodies should decrease and eventually normalize on a GF diet. This suggests reduced immune activation but doesn’t directly measure healing.

Biopsy

The gold standard. Follow-up endoscopy with biopsy shows actual intestinal structure. Some doctors recommend one at 1-2 years. Others only if symptoms persist.

What Sets Back Healing

Gluten exposure: Even amounts you can’t taste or see. The threshold is low (probably around 10-50mg daily can cause damage in some people).

Hidden gluten: Cross-contamination counts. That shared toaster matters.

Oats (for some): Even GF oats trigger immune response in a subset of celiacs.

Other factors: Severe stress, certain medications, infections may affect healing speed.

Supporting Healing

While the diet does the heavy lifting, you can support healing:

Nutrition: Work with a dietitian to address deficiencies. You may need supplements initially, especially:

• Iron
• Vitamin D
• B12
• Calcium
• Zinc

Rest: Healing takes energy. Don’t expect to function at 100% immediately.

Stress management: Chronic stress affects gut health and immune function.

Probiotics: Research is mixed, but some evidence suggests they may help gut recovery.

Patience: Healing isn’t linear. You may have good days and bad days. The trend is what matters.

The Reality of Incomplete Healing

Some people never achieve complete histological recovery despite strict diet adherence. This is frustrating.

Important to know:

• Significant improvement matters even without perfection
• Many people with incomplete histological recovery are asymptomatic
• Long-term outcomes are still better than undiagnosed/untreated celiac
• Research is ongoing into why some don’t heal completely

The Takeaway

Celiac disease causes real, measurable damage to your intestine. This isn’t imaginary or exaggerated. The damage is visible on biopsy.

The gluten-free diet allows healing. For most people, significant recovery happens within 1-2 years of strict adherence.

But “strict” means strict. Every exposure restarts the damage cycle. There’s no “mostly” gluten-free that works.

The science is clear: avoid gluten completely, give it time, and your body can heal. That’s the path forward.