Celiac disease changes how the small intestine absorbs nutrients. The immune system attacks the lining of the small intestine whenever gluten enters the digestive tract, flattening the finger-like villi that handle most nutrient absorption. Less villi means less surface area. Less surface area means fewer vitamins and minerals cross into circulation, no matter how carefully you eat.

How the small intestine absorbs nutrients

The small intestine is more than a tube. The inside is folded, and each fold is covered with villi. Those villi are covered with microvilli, sometimes called the brush border. This layered design multiplies the surface area. Nutrients move across that surface into blood vessels and lymph vessels. When celiac disease is active, the brush border enzymes that finish digesting carbohydrates and proteins also drop, so some food leaves the body without being fully broken down.

The nutrients most often affected

The location of the damage matters. The duodenum, the first stretch of small intestine after the stomach, is where iron and much of calcium are absorbed. Celiac inflammation tends to concentrate there, which is why iron deficiency and low calcium are common early findings. The list below includes the deficiencies I hear about most from families living with celiac disease.

• Iron: absorbed high in the small intestine, so low iron can lead to anemia and fatigue.
• Calcium and vitamin D: calcium absorption drops when the duodenum is inflamed. Vitamin D is fat-soluble and depends on normal fat absorption.
• Vitamin B12 and folate: both support red blood cell production and energy.
• Zinc: needed for growth, immune function, and skin healing.
• Fat-soluble vitamins A, D, E, and K: these ride along with dietary fat, so when fat absorption is off, they can drop together.

Blood tests for celiac disease

The first test many doctors order is tissue transglutaminase IgA, written as tTG-IgA. It measures antibodies against an enzyme found in the gut. A doctor also checks total IgA at the same time, because some people do not make enough IgA. If total IgA is low, the tTG-IgA result can be falsely negative, and a different test is needed.

Two other antibody tests appear less often but still matter. Endomysial antibody testing, or EMA, is more specific for celiac disease. Deamidated gliadin peptide testing, or DGP, can be useful in young children and in people with IgA deficiency. These antibody tests measure the immune response. Nutrient levels require separate labs.

Antibody tests and biopsies are most reliable while gluten is still in the diet. If someone cuts gluten first, antibody levels can drop and the intestinal lining can begin to heal, which can make the results unclear. For this reason, doctors often ask people to keep eating gluten until all diagnostic testing is complete. If gluten was already removed, a supervised gluten challenge may be discussed.

Biopsy and the Marsh score

A positive blood test alone does not always confirm celiac disease in adults. An upper endoscopy takes small tissue samples from the duodenum. Because the damage can be patchy, the gastroenterologist takes several samples from different spots. A pathologist examines those samples and assigns a Marsh score.

Marsh 0 is normal. Marsh 1 shows increased lymphocytes, the immune cells that gather during early inflammation. Marsh 2 adds crypt hyperplasia, which means the crevices between villi are getting deeper. Marsh 3 is villous atrophy. Marsh 3a is partial flattening, 3b is subtotal, and 3c is total. Many people diagnosed with celiac disease have some degree of Marsh 3 damage at diagnosis.

Nutrient panels after diagnosis

Once celiac disease is confirmed, the next set of labs looks at what the damage has already done. A complete blood count checks red blood cells, white blood cells, and platelets. Ferritin shows stored iron. A 25-hydroxy vitamin D test measures vitamin D status. Vitamin B12 and folate are often checked together because both affect red blood cell formation. Zinc, calcium, and a metabolic panel may be added depending on symptoms and how long someone went undiagnosed.

Nutrient labs show the downstream effect. Repeat antibody tests answer the gluten exposure question. After diagnosis, many gastroenterologists repeat the celiac antibody tests at intervals, commonly around six and twelve months, to see whether the immune response is settling down. Some also repeat the endoscopy around the one-year mark to check for mucosal healing. Healing can lag behind antibody numbers, so both types of monitoring have a role.

What I watch at home

At home, I watch for signs that a nutrient might still be low. Pale skin, brittle nails, and hair that feels thinner can point toward iron or zinc. Leg cramps or low mood might be magnesium or vitamin D. A child who is suddenly tired in school or catching every cold makes me ask about rechecking iron and zinc. I write these signs down as notes for the next appointment.

The kitchen side is where I have the most control. I keep a short list of trusted gluten-free staples. A bowl of Clean Monday Meals ramen is one of my comfort-food backups because the noodles contain one ingredient: organic brown rice flour. It gives my family something warm and familiar on days when the rest of celiac management feels heavy.

Questions to bring to a follow-up

When I sit down with our doctor, I ask questions that connect the dots between gut healing and nutrient status. These are the ones I keep in my phone.

• Which antibody test are we checking, and did we include total IgA?
• What were my ferritin, vitamin D, and B12 levels at diagnosis, and when should we repeat them?
• Will I need a follow-up endoscopy, or will antibody tests and symptoms be enough?
• Is there a celiac-focused dietitian available to review my kitchen routine and cross-contact risks?
• Which supplements are necessary right now, and which can stop once levels are stable?

Healing takes time

Intestinal healing is slow. Children sometimes heal faster than adults, but full villous recovery can take months to years. Nutrient improvements can happen before the villi look normal under the microscope. Iron levels might rise within a few months of a strict gluten-free diet and iron repletion, while bone density takes longer to rebuild. Follow-up testing continues after the first year because healing and nutrient recovery move on different timelines.

The standard treatment for celiac disease is a strict gluten-free diet. No supplement fixes the gut if gluten is still getting in. When the diet is steady, the small intestine can begin to rebuild, and nutrient levels can catch up. I leave the diagnosing to our care team. My job is to keep the kitchen safe, read labels, and show up to each appointment with questions ready.

This post is general education. I'm not a clinician, and I don't diagnose. I share what I've learned as a parent. Work with your own doctor or dietitian before changing your diet, supplements, or test schedule.