5 Reasons Leaky Gut Causes Thyroid Issues (#2 will surprise you)

There is a huge connection between leaky gut and thyroid issues. Believe it or not, the two go hand and hand and not only thyroid conditions but autoimmune conditions as well.

In this article, I am going to break down the top five reasons why leaky gut causes thyroid issues and why it is so important to address any type of gut issue such as leaky gut at its source. I will also talk specifically about how leaky gut can lead to Hashimoto’s Thyroiditis and then some steps that you can take today to heal the gut and take the right steps towards uncovering potential gut health issues.

To start, let’s jump right in and talk about why leaky gut is commonly associated with autoimmune disease.

#1 Leaky Gut is Often Associated with Autoimmune Disease

Did you know that it is impossible to have a healthy body without a healthy gut? This is because the gut houses nearly 70% of our immune system. More and more research is coming out on the importance of taking care of the digestive system as it plays an integral role in the overall health of our body, and this is especially true for anyone with any type of autoimmune condition such as Hashimoto’s Thyroiditis. With autoimmune conditions such as Hashimoto’s, there is a very large chance that leaky gut is also present as well. (1)

With leaky gut, those tight junctions in the gut become “leaky” and allow things like undigested food particles as well as other harmful toxins and microbes to enter your bloodstream. When this occurs, the immune system goes into high alert as what is being leaked into the bloodstream is recognized as a foreign invader. With the immune system being triggered, inflammation also sets in. Unfortunately, when leaky gut is not addressed and this pattern continues for long periods of time there is tremendous stress put on your immune system. After a period of time, your immune system may begin attacking your own body tissue unknowingly as it is so overworked and stressed from all the foreign particles coming in. This is where autoimmune disease can set in and things like Hashimoto’s can develop.

This is just one of the many reasons leaky gut causes thyroid issues and a major reason why it is so important to tackle leaky gut from a holistic approach to be sure it is being addressed appropriately. Overlooking leaky gut or being misdiagnosed could be the difference between catching it early enough to prevent an autoimmune condition or it getting bad enough to where autoimmunity sets in. This is also where functional medicine comes in as leaky gut is something that many functional medicine practitioners are very educated on and can help set you on a path to recovery and healing your gut.

#2 Leaky Gut Can Cause Vitamin & Mineral Deficiencies

One of the missing pieces many modern medical professionals miss when diagnosing leaky gut happens to be vitamin and mineral deficiencies. When a patient comes to my practice with a deficiency, looking at the gut is one of the things that I always address. Why? Because with conditions such as leaky gut there is a large possibility that the reason the deficiency is present is due to the fact that the body is not absorbing what it needs to appropriately. The answer could be leaky gut in many of these situations.

Ongoing inflammation in the gut can cause things like iron deficiency anemia, B12 deficiencies, as well as a number of different mineral deficiencies. These can cause things like fatigue, muscle pain, bone issues, and even hair loss. This is one of the reasons why leaky gut can cause thyroid issues. When the body is deficient in vitamins and minerals and particularly things like iron, and selenium, thyroid hormone balance can be thrown off.

The body needs iron in order to synthesize thyroid hormone so when anemia is present, patients could ultimately end up dealing with a thyroid condition. Selenium is another essential mineral for thyroid health and if one is deficient they can suffer from thyroid consequences. Selenium helps with the conversion of T4 to T3 and it is also an important mineral for overall immune health.

With any type of deficiency, your body is at risk for not performing at the optimal level that it needs to be to keep all body systems happy and healthy. If leaky gut is present it is essential to address it and get you on a path to health so that vitamin and mineral deficiencies do not occur and ultimately lead to complications with your thyroid health.

#3 Leaky Gut is Often Triggered by Inflammation

One of the causes of leaky gut happens to be inflammation. Inflammation can cause those tight junctions in the gut to become “leaky.” As we talked about before, once foreign particles begin leaking into the bloodstream, the immune system starts to make antibodies against what is viewed as foreign invaders. Your immune system begins to attack things like undigested food particles that may have never been an issue for you before, but now are being targeted as foreign since they are entering the bloodstream as larger molecules. This is also where food sensitivities set in for those with leaky gut.

The problem with these antibodies is that they can get into different tissues in the body and then trigger an immune reaction there as well. Next, autoantibodies may be created which can set you on a path for chronic inflammation. This is again where an autoimmune condition can occur. If the inflammation is triggered in the thyroid then Hashimoto’s or other thyroid diseases could occur. If the antibodies begin to attack the gut, gut conditions can arise. Any area of the body can be affected by leaky gut, it all depends on where the antibodies go and where the inflammation sets in.

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As you can see, it all began with inflammation. Leaky gut starts with inflammation and then ultimately triggers inflammation in various areas of the body leading to further complications and even autoimmune diseases. It is very important to work with a skilled practitioner if you suspect you may be dealing with leaky gut as it can be tricky to detect. Many times, someone can consume a reactive food and not have any type of reaction for 24 hours. This can make it difficult to pinpoint what is causing the reaction if you are unsure what to look out for. There may also be a number of foods causing a reaction and worsening leaky gut so I always like to take a thorough look at what my patients are eating and then look at potential inflammatory responses.

#4 Leaky Gut Can be Caused by Gluten Consumption Which is Also Linked to Thyroid Issues

Over the past couple of years, gluten free diets have become increasingly popular and I believe that they are here to stay. While some people may view gluten free diets as just another “fad diet” I think it is incredibly important for my patients to remove gluten from their diet lifelong and especially those who have leaky gut or a thyroid condition.

There are many things we need to worry about with gluten. For one, gluten can certainly lead to leaky gut. When we consume gluten, a chemical called zonulin is triggered and then released. Zonulin tells those tight junctions in your gut to open which can ultimately lead to leaky gut. (2) When these tight junctions open, gluten can pass through those junctions along with any other undigested food particles and microbes. For this reason alone, it is very important to keep gluten out of the diet and especially if leaky gut is suspected. Leaky gut can lead to autoimmune disease so we definitely do not want to include any foods that could potentially lead to thyroid conditions or other autoimmune disorders into our diet.

Secondly, gluten is also a major issue for anyone who suffers from a thyroid disease as gluten closely resembles your own body tissues including the thyroid. When gluten is consumed by someone with thyroid disease, the immune system will respond by destroying gluten especially in the case of leaky gut. However, the immune system may also end up attacking the thyroid as the immune system may mistake your thyroid for gluten molecules.

Another point I would like to talk about here is that gluten can cause inflammation and unfortunately, inflammation is the leading cause of nearly all disease. While inflammation is a necessary component of the immune system, and our bodies natural response to targeting anything that should not be in the body, chronic inflammatory states can lead to major issues like autoimmunity.

A large majority of the population suffers from a gluten sensitivity and many of these cases go undiagnosed. This means that each time someone consumes gluten who doesn’t know they have a sensitivity, inflammation is triggered. This can cause the immune system to go haywire and can lead to a state of chronic inflammation. The only way to give your immune system the break it needs to recover is to remove gluten from the diet. The trick here is that gluten must be removed completely. This is so important because as it turns out, gluten consumption can actually spike your gluten antibodies for three whole months! (2) This means that even eating it once in a while can lead to serious issues among those with a gluten sensitivity or Celiac disease.

The bottom line here is to remove gluten from the diet. Not only is it damaging for someone who already has a thyroid condition, but it can also cause leaky gut which is another cause of autoimmune disease so there is truly no reason we should have this food a part of our diet.

#5 The Gut Houses 70% of the Immune System

As I have already mentioned, the gut houses a large majority of our immune system. Without a healthy gut, it is nearly impossible to achieve overall health which is why an unhealthy gut can lead to thyroid issues.

The portion of the immune system that resides in the gut is referred to as the GALT which stands for gut-associated lymphoid tissue. The GALT is home to different types of lymphoid tissues that store things like immune cells and these immune cells will produce the antibodies that attack particles in the body that are recognized as foreign invaders. (3) This is a protective function of the gut but when leaky gut is present, this function doesn’t work the way that it should. When particles seep into the bloodstream, as you now know, the immune system starts to attack and then autoimmune diseases can arise. When the gut is unhealthy the body is unhealthy which is why it is so important to take the proper dietary and lifestyle steps necessary to protect these tight junctions in the gut and to allow the GALT to function the way it needs to in order to keep the body healthy.

If you suspect you may be dealing with leaky gut or you have a thyroid or other autoimmune condition, here are some steps you can take today to help heal the gut.

Hypothyroidism leaky gut

Steps to Heal Your Gut Naturally

There are several steps you can take to repair your gut and improve your overall health naturally Here is what I recommend:

Remove Food Sensitivities

Food sensitivities are one of the main reasons behind leaky gut syndrome and common chronic symptoms from digestive issues, headaches, skin problems to fatigue, anxiety and so on. I recommend that you get tested for food sensitivities and/or try an elimination diet to spot your food sensitivities. 

Get Tested for Gut Infection and Leaky Gut

I recommend that you work with a functional health practitioner, like myself, and get tested for gut infections and leaky gut syndrome. They will be able to help you with an individualized plan to tackle your gut sensitivities and leaky gut through gut-supporting nutrition, supplementation, and lifestyle strategies.

Eliminate Inflammatory Foods

Eliminate refined sugars, refined oil, processed foods, and artificial foods. Eliminate deep-fried foods and junk food. Cut out gluten, grains, and dairy. Remove all foods that you are sensitive or allergic to.

Eat an Anti-Inflammatory Diet

Eat plenty of greens, vegetables, herbs, spices, and low-glycemic index fruits. Enjoy more grass-fed animal products and wild-caught fish. Drink bone brought regularly to support your gut lining. Enjoy more fermented vegetables, such as kimchi, sauerkraut, coconut kefir, and kombucha to support healthy gut flora. Add anti-inflammatory coconut oil to your diet to help fight inflammation and viral, bacterial, and fungal overgrowth.

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Reduce Chronic Stress

Reduce any sources of chronic stress and learn to respond to stress better. Spend time with supportive and uplifting people. Schedule regular me-time. Practice meditation, breathwork, journaling, gratitude, and yoga. Exercise regularly and spend plenty of time in nature.

Reduce Environmental Toxicity

Eliminate as many environmental toxins as possible. Avoid conventional cleaning, body, and beauty products, and choose organic, natural, and DIY alternatives. Improve your air quality with HEPA filters and having indoor plants in your home. Make sure your home is free of mold. Drink purified filtered water. Avoid plastic as much as possible, and use glass or aluminum bottles, glass jars and boxes, cloth bags, wooden or ceramic bowls, and other plastic-free options. If you are a smoker, stop smoking and avoid second-hand smoke.

Try a 30-Day Thyroid Reset

If you have thyroid imbalances or thyroid disease, I recommend reading and following the recommendations in my book, The 30-Day Thyroid Reset Plan: Disarming the 7 Hidden Triggers That are Keeping You Sick. This plan will help you to improve your gut health, repair your thyroids, and improve your overall health. You will learn everything you need to know about thyroid disease. I offer a 30-day plan to improve your health and my favorite thyroid-friendly recipes to nourish your body with delicious meals.

Hypothyroidism leaky gut

Final Thoughts

Your gut health and thyroid health are both important for your overall health. They come hand in hand and are closely connected. If you have leaky gut syndrome or other gut health issues, it is important to address it right away to avoid thyroid problems. If you have thyroid issues, it is important to uncover and address underlying gut health issues and leaky gut syndromes. Follow my tips to improve your gut health naturally.

If you are dealing with symptoms of leaky gut syndrome, Hashimoto’s disease, or other thyroid issues, I invite you to schedule a consultation with me. I can help to identify the root cause of your condition and recommend a personalized treatment plan to repair your body and regain your health and well-being. Schedule your consultation here.


(1) Amy Myers. Understanding the True Cause of Autoimmune Disease

(2) Amy Myers. 3 Important Reasons to Give up Gluten if you have an Autoimmune Disease

(3) Chris Kresser. The Thyroid-Gut Connection

5 Vitamin and Mineral Deficiencies Common in Thyroid Conditions. Natural Endocrine Solutions

— Update: 03-01-2023 — cohaitungchi.com found an additional article Why Leaky Gut and the Thyroid Don’t Work Well Together from the website www.tamparejuvenation.com for the keyword hypothyroidism leaky gut.

What is a Leaky Gut?

When the human intestines are healthy and functioning correctly, they act as both a barrier and filter for our bodies. They essentially are supposed to allow nutrients to be absorbed in the gut but to block any toxins that may be circulating within the body. When the intestines are not working properly, it can cause the body to absorb the toxic substances into the bloodstream and may result in inflammation as your body attempts to attack these foreign invaders. Factors that may cause intestinal permeability can include food sensitivities, stress, and nutrient deficiencies. Patients may be experiencing symptoms such as chronic inflammation, joint pain, foggy thinking or bowel diseases. Learn more about leaky gut.

Gut and Thyroid Connection

There is a strong correlation between thyroid and gut health. Studies have shown that low thyroid hormones can lead to leaky gut and poor gut health can suppress thyroid function. Optimal digestion actually helps to tame the antibodies associated with autoimmune conditions such as Hashimoto’s and Graves.

Hashimoto’s Thyroiditis

Characterized by the immune system’s attack on the thyroid gland, Hashimoto’s thyroiditis is one of the most common autoimmune diseases. Women often experience Hashimoto’s more often than men but both may complain of symptoms such as unexplained weight gain, fatigue, or hair loss. 

Studies have shown the prevalence of autoimmune thyroid disease in patients with celiac disease was about four times higher than that in the general population. In a study with Dutch patients, researchers found that of 184 patients with celiac disease, 21% of them were positive for a thyroid disorder. 

What can you do?

Studies have clearly shown the link between Hashimoto’s and gluten intolerance. A study published in the Journal of Digestive Diseases and Sciences found that in patients with celiac disease, intestinal permeability returned to normal in 87% of people who followed a gluten-free diet for over a year. Improving your diet and being conscious of what foods you are consuming can help treat your leaky gut. 

Eating items such as processed foods, too much sugar, and foods you are sensitive to can worsen your leaky gut. By eliminating these products as well as gluten from your diet, you can help reduce the inflammation in the body and allow the gut to heal. 

Eliminate known foods that cause sensitivities or intolerances and stay away from pesticides and processed vegetable oils. Typical problem foods you may want to  eliminate include:

  • Wheat
  • Dairy
  • Eggs
  • Nuts
  • Soy
  • Alcohol
  • Caffeine

While you eliminate these problem foods, you should also be adding foods into your diet to help heal the gut lining. Focus on adding in fibrous fruits, veggies, and beans to help enhance butyrate production. 

Foods high in Omega-3’s can help reduce inflammation in your intestinal cells and consuming bone broth can help the cells to stay strong. Foods to focus on should include:

  • Unprocessed meat and seafood
  • Healthy fats from coconut oil, high omega-3 foods, olive oil, and avocado.
  • Non-starchy veggies such as leafy greens
  • Fresh fruits

It is vital to focus on stress management while also changing your diet to help prevent any further digestive problems. Try avoiding stressful people and situations and find proper stress coping mechanisms to deal with any stress heading your way. It is also important to drink plenty of water and get your sleep!

After you have eliminated the common problematic foods, you can try to re-introduce certain ones back into your diet. Reintroduce one new food into your diet every 3 days and take note of any reactions your body has. 

Foods to reintroduce can include eggs, nuts, dairy or alcohol/caffeine, just make sure to only introduce one at a time. If you experience any symptoms after introducing a specific food, stop consuming it for good until you’ve spoken with a practitioner or nutritionist. 

How Tampa Rejuvenation Can Help

Patients often complain of thyroid disorder symptoms and do not feel better after speaking with their primary care physicians. This is typically because most practitioners will prescribe a synthetic T4 for hypothyroid patients. 

This approach will not work for patients who have trouble converting T4 to T3 and most will feel better when both T4 and T3 are replaced. It is important to work with a hormone clinic that specializes in thyroid disorders, such as Tampa Rejuvenation, in order to figure out exactly what is going on so that we can get you feeling better. 

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We do in-depth bloodwork to get these answers and then our practitioners can come up with an individualized treatment plan for treating your thyroid concerns. Working alongside the practitioner, our nutrition team can help you incorporate a diet into your lifestyle that will help improve thyroid and leaky gut symptoms. 

— Update: 04-01-2023 — cohaitungchi.com found an additional article 5 Ways For Healing Leaky Gut from the website drbrighten.com for the keyword hypothyroidism leaky gut.

You may have heard that leaky gut syndrome is why you developed hypothyroidism in the first place. Leaky gut syndrome is involved in the development of hypothyroidism or more specifically, autoimmune hypothyroidism  (Hashimoto’s) in the majority of cases. Here are those connections and 5 ways for healing leaky gut!

Hashimoto’s thyroiditis is the number one cause of hypothyroidism in the United States. And while not all causes of hypothyroidism are well understood, we do know that if you have an autoimmune condition, then your immune system is not behaving as it should.

And where is the majority of your immune system located? Your gut!

Could leaky gut syndrome be the cause of your hypothyroidism? Click To Tweet

Autoimmunity, Leaky Gut Syndrome & Hypothyroidism

Doctors estimate that your gut houses anywhere from 70-80% of your immune system. This aspect of the immune system, known as the gut associated lymphoid tissue (GALT), can become triggered by infectious agents, food particles, and other proteins that make their way through the lining of the intestine in a condition known as “leaky gut.” Exposure to these “non-self” proteins or antigens stimulates the immune system to produce antibodies.

The job of antibodies is to tag foreign proteins for destruction. However, in the case of molecular mimicry, the amino acid sequence of the non-self protein that has been tagged for destruction closely resembles an amino acid sequence of self proteins, a.k.a. your body tissues. When this happens, your immune system can mistake your tissues as foreign and begin to attack the target tissue, in addition to causing inflammation in the body.

This how leaky gut can cause you to develop antibodies to your thyroid.

The job of the gut mucosa or intestinal lining is to allow nutrients to pass through for absorption and utilization in the body. At the same time, the intestinal lining should keep harmful proteins from entering. But in cases of leaky gut, these proteins are able to cross this protective barrier and trigger an inflammatory response.

Over time, after repeat exposure, the body will respond by creating antibodies, which can set off a cascade of autoimmune destruction of the thyroid tissue — resulting in Hashimoto’s and eventually hypothyroidism.

What Causes Leaky Gut Syndrome:


Long-term, regular  use of NSAIDs (non-steroidal anti-inflammatory drugs) like ibuprofen can cause damage to the intestinal lining.

Antibiotic Use.

Antibiotics disrupt the normal healthy bacteria in your gut and leave it susceptible to harmful organism overgrowth.

Mom’s exposure to antibiotic due to C-section or Group B Strep will cause disruption of both mom and baby’s gut. Antibiotic use in general can disrupt intestinal flora and gut lining for 6-12 months.

Birth Control Pill.

Chronic Stress.

Stressors from work, life, and even exercise or strict dieting can alter your microbiome and lead to leaky gut. Learn how to de-stress today.

High Sugar Diets.

Diets high in processed grains and sugars can lead to damaging hormonal swings, not to mention feed yeast, bad bacteria, and pathogens in the gut. There are so many reasons to cut down on the sugar.

Low Fiber Diets.

Diets rich in fiber, both soluble and insoluble, have been shown to reduce the risk of developing many gut pathologies, including leaky gut.

5 Ways to Heal Leaky Gut Syndrome for Hypothyroidism

#1 Test! Don’t Guess!

If you think you may have intestinal permeability, contact your doctor and discuss these tests:

  • IgG and IgA Food Intolerance Testing: Leaky gut can cause an array of food intolerances. Learn more about food intolerance testing here.
  • Intestinal Antigenic Permeability Screen: A simple blood test to evaluate intestinal permeability to large molecule which inflame the immune system.
  • Urine Test: After drinking a carbohydrate solution you will need to collect your urine for 6 hours. Urine that contains high amounts of the sugar indicates a positive for leaky gut.
  • Stool Culture and/or SIBO Testing (Lactulose Breath Test): Gut infections or bacterial or yeast overgrowth can make intestinal permeability worse. It’s important to dig deep to find the root cause of your condition.

#2 Figure Out Food Intolerances

An elimination diet can help you determine if you have food sensitivities that are making you feel ill.  

We use the following therapeutic diets in my practice when helping people determine their sensitivities.

  • Anti-inflammatory
  • Autoimmune Protocol (AIP)
  • Basic Elimination Diet: eliminating the top 8 allergens

In my clinical practice I have all of my patients work with my Functional Medicine Nutritionist during an elimination diet to not only help us get the best data, but to also support my patients in the journey. They are trained experts in thyroid nutrition and design their meal plans to deliver the most thyroid supportive foods during the elimination phase and beyond. 

#3  Get the Thyroid On Point!

#4 Try Healing Herbs

Slippery elm, aloe, DGL, turmeric and marshmallow root can help heal the intestinal lining and as part of a comprehensive treatment plan, they can help you resolve leaky gut.

#5 Eat Your Probiotics

Beet kvass, kombucha, sauerkraut, kimchi, turmeric root, ginger and lots of plant based foods give your gut and microbiome what it needs to heal and function optimally.

And while you’re at it…Drink Bone Broth!!! Bone broth is one of the most healing foods that you can consume when you are aiming to heal leaky gut. In my practice I recommend patients make their own with this recipe or purchase a quality bone broth from a local store or online retailer like Kettle & Fire.

Leaky Gut Syndrome and hypothyroidism can be a lot to navigate on your own. Partnering with an expert such as a Functional Medicine practitioner will help you understand the specific needs of your body and help you create an individualized plan for healing.

Wast this helpful for you? Reach out to me on my Facebook page and let me know if you’ve been struggling with this or have possibly been misdiagnosed. I’m here to help you.

Related product: Women’s Probiotic


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About the Author: Tung Chi