Going gluten and dairy-free to help heal Hashimoto's

Read more about the connection between gluten, dairy, and Hashimoto's.

This is a re-post from Dr. Pooja Mahtani, one of Pollie's advisors. To view the original pieces, visit her website, here! Dr. Pooja Mahtani is the founder of Pooja Mahtani Wellness, a virtual functional nutrition practice that specializes in gut, immune, and hormonal health. Dr. Mahtani is a Board Certified Nutrition Specialist® and Licensed Dietitian Nutritionist. She also holds a Doctorate in Pharmacy and Master’s in Human Nutrition along with extensive training in functional nutrition from the Institute for Functional Medicine.

Eliminating entire food groups from your diet may sound extreme. However, for people with Hashimoto’s thyroiditis, going gluten and dairy-free may drastically improve their thyroid-related symptoms.

This article will explain the benefits of going gluten and dairy-free, as well as the science behind this dietary approach to healing Hashimoto’s disease.

What is Hashimoto’s Thyroiditis?

Hashimoto’s thyroiditis is an autoimmune disorder that affects the thyroid gland, which is in charge of producing thyroid hormones that help regulate a multitude of functions such as metabolism, energy production, body temperature, weight, and more. This disease affects 14 million people in the United States, and women are seven times more likely than men to develop Hashimoto’s disease. 

In this condition, the immune system creates antibodies that attack thyroid cells as if they were a foreign body. The immune system wrongly enlists disease-fighting agents that damage the thyroid and eventually cause thyroid gland destruction.

Here are some common signs of Hashimoto’s disease: 

  • Fatigue 
  • Increased sensitivity to cold
  • Dry skin
  • Brittle nails
  • Hair loss
  • Thinning eyebrows
  • Constipation (often severe)
  • Muscle weakness
  • Joint pain and stiffness
  • Irregular periods
  • Infertility
  • Depression
  • Brain fog

On a related note, most people with hypothyroidism, a condition caused by an under-active thyroid, also have Hashimoto’s disease. In fact, it is believed that up to 90% of hypothyroid cases are indeed autoimmune in nature. 

If you have been diagnosed with hypothyroidism, I urge you to also get tested for Hashimoto’s disease. Unfortunately, most doctors do not run the additional antibody tests needed to diagnose Hashimoto’s disease because their treatment approach is the same regardless of whether you have hypothyroidism or a concurrent autoimmune presentation: synthetic thyroid hormone medication.

The connection between food sensitivities and Hashimoto’s

Hashimoto’s and food sensitivities often go hand-in-hand due to the inflammatory response of the immune system. Here’s what you need to know about food sensitivities and Hashimoto’s disease. 

Food sensitivity vs. food allergy

First, it’s important to note that a food sensitivity is not the same as a food allergy. 

A food allergy is an immune system reaction that can occur within minutes to hours after eating a certain food that your body has identified as a “foreign invader.” It will mount a response by producing antibodies called immunoglobulin E (IgE). 

These IgE antibodies will go on to elicit an allergic reaction that can range from mild to life-threatening anaphylaxis. Symptoms of food allergies include wheezing, hives, itchiness, skin swelling, vomiting, and diarrhea. 

On the other hand, a food sensitivity is an immune system reaction that is often delayed in nature, occurring hours to several days later. Instead of triggering an IgE-mediated response, a sensitivity is caused by immunoglobulin G (IgG) and immunoglobulin A (IgA) antibodies. 

These IgG and IgA antibodies can travel throughout the body and cause widespread symptoms like digestive upset, joint pain, headaches, fatigue, rashes, dizziness, and brain fog. Food sensitivity reactions are not usually life-threatening in nature.

The two most common food sensitivities today are gluten and dairy. Let’s explore the science behind this modern-day phenomenon. 

Leaky gut and food sensitivities

Food sensitivities can cause and exacerbate intestinal permeability, which is also known as leaky gut. Leaky gut is a digestive issue where the intestinal lining becomes inflamed and porous. This porous, or “leaky,” lining then allows bacteria, undigested food, toxins, and other foreign invaders to enter the bloodstream, triggering an inflammatory response from the immune system. 

Food sensitivities are part of a continuous cycle where food particles penetrate the porous intestinal lining, promote inflammation (due to immune system activation), and contribute to further intestinal permeability or leaky gut.

Leaky gut is often a precursor to a potential autoimmune disease. In individuals with genetic predispositions, a leaky gut may trigger and promote an environment for autoimmune diseases like Hashimoto’s thyroiditis to develop.

Some common causes of leaky gut include:

  • Gluten
  • A diet high in refined sugars and unhealthy fats
  • Low stomach acid
  • Chronic stress
  • Frequent alcohol intake
  • Frequent use of medications like ibuprofen

Related Post: Have Food Sensitivities? Your Hormones May Be Playing a Role.

Molecular mimicry

As mentioned, leaky gut is usually the gateway to developing autoimmune disease. Once partially digested food crosses the intestinal lining, the immune system gets involved. 

In fact, the immune system will begin to memorize the protein sequence of the undigested food to defend against it in the future. Problems begin to worsen when a foreign invader's molecular structure and protein sequence are similar to those of your own body’s tissue. 

When this happens, the immune system is fooled into attacking a similar protein sequence that is actually part of your body’s tissue, leading to an autoimmune disease. This phenomenon is known as molecular mimicry. 

To put it into perspective, the molecular structure of gliadin and casein, proteins found in gluten and dairy, respectively, is very similar to that of transglutaminase, an enzyme that is abundant in both the GI tract and thyroid. 

When you have a leaky gut, gliadin and casein enter the bloodstream as foreign invaders. These proteins trigger the immune system to produce antibodies that then attack and destroy them. 

Consequently, due to molecular mimicry, these same antibodies designed to target gliadin and casein end up attacking your thyroid. In other words, your thyroid issue gets caught in the crossfire between the immune system and “foreign” food proteins. 

Over time, if gluten and dairy continue to be part of your diet, the immune system will continue to attack your thyroid gland, leading to the eventual destruction of the thyroid gland and development of Hashimoto’s disease.

Related Post: How Hormones and Gut Health Impact Your Immune System. 

Do I Need to go gluten and dairy-free to heal Hashimoto’s? 

For most people, the answer is yes. Gluten and dairy are two of the most common inflammatory foods in modern times, and they frequently trigger leaky gut.

Recall that leaky gut is a precursor to autoimmunity and often triggers and exacerbates the symptoms of Hashimoto’s disease. 

While research around the gut-thyroid axis is still emerging, scientific evidence to date demonstrates a clear relationship between food sensitivities and thyroid health. The evidence around gluten and dairy-free diet benefits are outlined in the next section.

Gluten and dairy-free diet benefits for Hashimoto’s 

Preliminary research is beginning to show a strong relationship between diet and autoimmune disease. Here are a few gluten and dairy-free diet benefits, according to the latest studies:

  1. Eliminating gluten from your diet may reduce thyroid antibodies.
  2. Eliminating dairy from your diet may decrease TSH levels.
  3. Removing food sensitivities may help reduce inflammation and Hashimoto’s symptom flares.

For many people, removing gluten and dairy from their diet will help to heal the gut lining, reduce an overly activated immune system, and ultimately reverse the symptoms of Hashimoto’s disease.

Risk factors of going gluten and dairy-free 

Implementing a gluten and dairy-free diet, like any diet, is associated with a higher risk of nutrient deficiencies. 

Working with a functional medicine nutritionist can help you successfully manage your new diet and identify any potential nutrient deficiencies through a comprehensive nutritional assessment and lab work. 

Will I ever be able to eat gluten or dairy again?

To maintain the benefits of this diet, most people with Hashimoto’s disease should continue with a gluten and dairy-free diet. While some people may be able to add gluten and dairy foods back to their diets, the majority of people will experience a return of Hashimoto's symptoms.

If you believe you have healed your leaky gut, you can always reintroduce small amounts of gluten (like sourdough bread) or organic pasture-raised dairy and see how you feel.

With that said, each person is unique, and no “one-size-fits-all” diet will heal everyone. Experiment with what foods do and don’t work for you, and tailor your own diet to a way of eating that makes you feel great. 

A functional medicine approach to Hashimoto’s Disease

If you have Hashimoto’s disease, you will likely experience gluten and dairy-free diet benefits. In addition, a functional medicine approach to healing Hashimoto’s thyroiditis may help manage your symptoms further and restore your quality of life. 

Functional Testing

When utilizing a functional medicine approach to address Hashimoto’s disease, the first step includes running a comprehensive thyroid panel and assessing for any nutritional deficiencies and food sensitivities. Many times, additional functional testing to assess your adrenal and gut microbiome status is also necessary to get a full picture of your current state of health.


After your thyroid, gut, and adrenal status have been analyzed, an elimination diet is often the first intervention to start the healing process. An elimination diet is a short-term diet to discover your personal thyroid diet, which often includes removing gluten and dairy foods.

Nutritional Supplementation

In addition to a personalized thyroid diet, a tailored supplementation plan can go a long way in addressing thyroid-related nutrient deficiencies, reducing thyroid antibodies, normalizing TSH levels, and boosting overall thyroid health.

Related Post: Best Herbs for Thyroid Health


Finally, the functional medicine approach also addresses lifestyle factors like exercise, chronic stress, poor sleep, and environmental toxin exposure. Optimizing lifestyle is critical to thyroid health.

Work with a functional medicine nutritionist 

Your thyroid performs a vital function for your health and overall well-being. When it’s not operating correctly, it can be the root of many symptoms, such as fatigue, weight gain, irregular periods, and infertility. 

While medication is sometimes necessary to restore thyroid function, diet and lifestyle play a crucial role in overcoming Hashimoto’s thyroiditis. In fact, most of my Hashimoto’s clients experience gluten and dairy-free diet benefits. When we layer in targeted supplement and lifestyle recommendations, clients often go into disease remission as well.

Dr. Pooja Mahtani

MS, CNS, LDN, PharmD

Dr. Pooja Mahtani is the founder of Pooja Mahtani Wellness, a virtual functional nutrition practice that specializes in gut, immune, and hormonal health. Dr. Mahtani is a Board Certified Nutrition Specialist® and Licensed Dietitian Nutritionist. She also holds a Doctorate in Pharmacy and Master’s in Human Nutrition along with extensive training in functional nutrition from the Institute for Functional Medicine.