Diet and Hashimoto’s Disease: Do You Need to Eliminate Dairy and Gluten?

Elimination Diets and Hashimoto’s Disease

Nowadays, it is quite common to see recommendations for eliminating gluten and lactose in cases of hypothyroidism and Hashimoto’s disease. This is due to the increasing prevalence of thyroid disorders and patients’ growing interest in supporting their treatment and improving well-being.

Hashimoto’s Disease and Gluten Intolerance

For patients with autoimmune thyroiditis (including Hashimoto’s), it may be worthwhile to expand diagnostic testing to check for celiac disease. These two autoimmune conditions can co-occur due to their shared pathophysiological background.

One theory suggests that gliadin—a protein fraction of gluten—resembles thyroid tissue in structure. In people with celiac disease, the immune system produces antibodies against gliadin, which may mistakenly attack thyroid structures and cause tissue fibrosis.

A gluten-free diet can help inhibit this process. Eliminating gluten in such cases may reduce immune system stimulation.
However, there is still insufficient scientific evidence to support routinely using a gluten-free diet in Hashimoto’s. It should primarily be considered for individuals with confirmed celiac disease.

How to Check for Celiac Disease or Gluten Intolerance

If you have Hashimoto’s, it may be helpful to determine whether you also have gluten intolerance or celiac disease. These two conditions are not the same—celiac disease affects the entire body, while gluten intolerance or allergy is more common.

Celiac disease is a genetic condition. For this reason, genetic tests for HLA-DQ2 and HLA-DQ8 antigens are increasingly performed. The presence of these antigens indicates a predisposition to developing celiac disease.

If these antigens are absent, celiac disease is unlikely. In that case, further testing can be done for gluten sensitivity or allergy.

Current guidelines recommend serological testing—analyzing blood samples—to detect antibodies such as:

• anti-tissue transglutaminase (tTG), 
• deamidated gliadin peptides (anti-DGP), 
• anti-endomysial antibodies (EmA). 

The most reliable markers are tTG and DGP. Testing also includes total IgA and IgG levels, followed by determining the presence of the above antibodies in the same class.

In some cases, a small intestine biopsy is performed to evaluate characteristic histopathological changes in the intestinal mucosa. These are assessed using the modified Marsh classification.

If celiac disease is ruled out but symptoms persist, food intolerance tests can help assess whether gluten should be eliminated.

Hashimoto’s Disease – Is Dairy Elimination Necessary?

Lactose intolerance affects around 30% of adults in Poland. It is mainly caused by a deficiency of lactase—an enzyme that breaks down lactose into simple sugars.

Without lactase, lactose remains undigested, increasing osmotic load and water content in the intestines, which can lead to diarrhea. Additionally, undigested sugar ferments in the colon, producing short-chain fatty acids and gases. Symptoms include:

• abdominal discomfort, 
• stomach pain, 
• nausea, 
• bloating, 
• intestinal cramps, 
• headaches. 

A lactose-free diet in patients with Hashimoto’s and lactose intolerance can help reduce TSH levels.

Lactose Intolerance and Thyroid Medication Absorption

Lactose intolerance can interfere with the absorption of medications, including levothyroxine used in treating hypothyroidism. Studies show that lactose-intolerant individuals sometimes struggle to absorb this medication properly.

In such cases, increasing the dose may be necessary. However, eliminating lactose can improve TSH levels even without changing the dosage.

Thyroid Inflammation and Casein

Some researchers are investigating whether there is a link between casein (found in milk and dairy products) and thyroid inflammation. Eliminating dairy should be considered individually, weighing the potential risks and benefits.

For patients with both Hashimoto’s and confirmed lactose intolerance, the recommendations are similar to those for gluten elimination: a lactose-free diet may be beneficial. However, dairy should not be eliminated routinely without medical justification.

How to Check for Lactose Intolerance

There are several ways to determine if you are lactose intolerant:

• Hydrogen breath test
  This test involves consuming a specific dose of lactose, then measuring hydrogen levels in exhaled air at several time points. Elevated hydrogen suggests improper lactose digestion. 
• Dietary history and symptom tracking
  A well-conducted dietary interview and symptom improvement after a 2-week lactose-free diet can help confirm the diagnosis. 
• Lactase enzyme level testing
  This invasive test analyzes enzyme levels in samples taken from the intestine. It is considered the most accurate method, though rarely used due to its invasiveness. 

Diet in Hashimoto’s Disease: After Elimination – What Next?

Remember, elimination diets don’t just remove certain foods—they require proper replacements.

What to Replace Gluten With?

People with confirmed celiac disease or gluten allergy must strictly avoid gluten—even in trace amounts. Their diet must be diverse and well-balanced.

Relying solely on processed gluten-free products can lead to overconsumption of artificial additives, simple sugars, and saturated fats—not recommended for thyroid conditions.

Instead, use naturally gluten-free grains (e.g., quinoa, buckwheat, tapioca, amaranth) and unprocessed whole foods like vegetables, fruits, meat, fish, nuts, seeds, and plant oils.

What to Replace Dairy With?

For lactose intolerance, choose lactose-free dairy products. These are nutritionally similar to regular dairy, with the lactose already broken down or probiotic bacteria added.

People following a dairy-free diet may also use fortified plant-based milk alternatives. Pay attention to the ingredients—many are sweetened for better taste. Avoid highly processed options with long ingredient lists.

Completely removing dairy can lead to mineral deficiencies, particularly calcium, which is best absorbed from dairy.

Good calcium sources include:

• Fortified plant products, 
• Low-oxalate vegetables: kale, turnip greens, Chinese cabbage, broccoli, savoy cabbage, soybean sprouts, pak choi (with up to 50% absorption), 
• Other plant-based sources: white beans, almonds, tahini, figs, oranges, sesame seeds, poppy seeds, sunflower seeds, chickpeas (15–20% absorption). 

Elimination Diet and Hashimoto’s Disease

Currently, there is no strong scientific evidence to support using elimination diets in all cases of Hashimoto’s disease. Patients should undergo diagnostic testing before making dietary restrictions.

The foundation of a Hashimoto’s diet remains a well-balanced nutrition plan based on healthy eating principles, enriched with essential micronutrients.

So, if you only have Hashimoto’s disease, an elimination diet is not necessary. But if you suspect gluten or lactose sensitivity, it’s worth getting tested. If tests confirm celiac disease, gluten intolerance, or lactose intolerance, then an elimination diet should be implemented.