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How to Fix Leaky Gut and Stomach Issues That Comes with Hashimoto’s

by | Jan 12, 2023 | Symptoms

Leaky gut is one of the biggest root contributors to autoimmunity, including Hashimoto’s. Many Hashimoto’s patients also struggle with digestive issues, which go hand in hand with a leaky gut. 

To put your Hashimoto’s and the associated digestive problems like bloating, post-meal discomfort, and constipation into remission, you need to heal your leaky gut. In this article, we’ll cover the evidence-based links between Hashimoto’s and these gut issues, along with solutions that work. 

By addressing the root causes, you can restore your gut health and eliminate most symptoms naturally. However, it typically won’t be a quick or easy fix, so we recommend working with a naturopathic or functional medicine doctor.  

How leaky gut and thyroid autoimmunity intertwine

To develop an autoimmune disease, you need to have 3 things [1]:

  1. A genetic tendency
  2. A leaky gut
  3. An environmental trigger, which can be a stressor, food, mold exposure, or infection

What is a leaky gut?

A leaky gut or intestinal permeability means your gut barrier allows more things through it than usual. A healthy gut barrier allows water and fully digested nutrients, such as amino acids, simple sugars, vitamins, and minerals through. Whereas, a leaky gut may allow partially digested food fragments and bacteria parts through as well.

Leaky Gut

Your gut barrier consists of a single cell layer, the mucus that covers it, and the immune system that works with your gut barrier.

When you have a leaky gut, whatever leaks through is exposed to your immune system. It then perceives your gut contents as foreign and starts to respond 

Because 70-80% of your immune system is in your gut, the gut is the largest interface between your body and the outside world [2]. This is why inflammation that starts in the gut can affect your entire body. 

The gut barrier inflammation can also affect nutrient absorption, which can lead to nutrient deficiencies such as iron and vitamin B12.

Does a leaky gut always cause autoimmune conditions like Hashimoto’s?

Autoimmune diseases are always multifactorial, so a leaky gut alone doesn’t automatically cause problems or diseases. Healthy people open and close their gut barriers multiple times a day with things like gluten, stress, and lectins.

Consider two scenarios here.

Scenario A: If your gut and immune system are perfectly healthy, then:

    1. Your gut barrier can reseal itself.
    2. Your immune system recognizes the food particles and low levels of bacteria toxins as harmless and chooses to ignore these [3,4]. In immunology, this is called “tolerance.”
    3. Your immune system readily kills immune cells that attack anything resembling your own cells. [5]

Scenario B: If you have a genetic tendency for autoimmunity and other life stressors that further throw things off, you can have:

    1. A gut that cannot repair itself fully, whether due to genetics, nutrition, infections, or stress.
    2. An immune system that loses its tolerance to food and bacterial toxins, instead responding with inflammation and remembering things it should ignore. The inflammation from this step also keeps the gut from fully repairing itself.
    3. Your immune system fails to eliminate self-attacking immune cells.

Key insight #1: Leaky gut is a major contributor to Hashimoto’s and related digestive problems. Healing a leaky gut is a key to putting Hashimoto’s into remission.

With #1 and #2 in scenario B, a leaky gut can cause common inflammatory health issues such as skin problems, fatigue, chronic pain, and irritable bowel syndrome, depending on where the weak links are in your body. 

Autoimmune diseases involve multiple factors, as when all three things happen in scenario B. You develop Hashimoto’s because all three unlikely things come together and lead to Hashimoto’s. A leaky gut can very well incite Hashimoto’s, given other risk factors, and Hashimoto’s can make a leaky gut worse [6]. So, it’s critical to break this vicious cycle to put your Hashimoto’s into remission.

What causes a leaky gut and how to heal it in Hashimoto’s

Anything that throws off the balance of your gut flora and creates gut inflammation will contribute to a leaky gut. Consider the following factors and address them:

Identify food sensitivities, allergies, and intolerances

An IgE antibody blood test will identify true allergies. Many IgE food panels include most foods you’d want to consider. Keep in mind that most food allergic reactions are severe and immediate, such as hives, itchiness, swelling, airway closure, or anaphylactic shock. So, most people would already know their food allergies. 

Food sensitivities and intolerances are a bit harder to identify because most tests, including IgG and IgA, have limited accuracy.

The best way to identify a food sensitivity or intolerance is by doing an elimination-challenge diet. You remove common inflammatory foods for 2 – 4 weeks before bringing them back one at a time. If symptoms get worse, then the food is the culprit. 

Eradicate chronic gut infections 

Gut infections are quite common among people with Hashimoto’s. Some gut infections such as Helicobacter pylori, bad bacteria, and parasites can keep your gut leaky and your gut flora unhealthy. 

Testing for and eradicating these chronic infectious organisms with the help of a holistic health provider is often key to healing a leaky gut. In fact, there are some case reports of people significantly improving Hashimoto’s after killing parasites like Blastocystis [7,8]. 

Balance gut flora

Your gut is home to thousands of different organisms, including bacteria, viruses, and yeast that intertwine with your health. Dysbiosis or an imbalanced gut flora intertwine with a leaky gut [9]. 

Ask your holistic doctor to perform a stool test such as GI-MAP to look for dysbiosis. Also, any digestive or inflammatory symptoms such as bloating, indigestion, stomach pain, or even skin and joint issues, tend to correlate with dysbiosis.

Common, basic approaches for dysbiosis include addressing everything mentioned in this article: you need to heal a leaky gut as an inflamed gut will feed bad bacteria [10]. Then, add probiotics and feed them with prebiotics (fibers and carbs that feed the probiotics) and plant antioxidants. 

Reduce or eliminate alcohol

Alcohol itself causes leaky gut and dysbiosis [11]. It also reduces gut movement, especially at concentrations above 15% [12]. This is why drinking, especially regularly, can throw off your gut health even further. Many holistic providers will recommend getting off alcohol completely during gut healing programs. 

Address head injuries (even very old ones)

Concussions and mild traumatic brain injuries can cause a leaky gut [13]. Also, an unhealthy microbiome, chronic inflammation, and a leaky gut may explain why some concussion cases become chronic, as in post-concussion syndrome [14]. 

Concussions even from decades ago can be contributing to your leaky gut and digestive problems. Many people don’t remember the concussions they got during infancy or childhood. Consider seeing a post-concussion syndrome specialist if head injuries could be a factor, or if you also struggle with brain function, memory, and depression. 

Key insight #2: I recommend seeing a practitioner to address a leaky gut by removing inflammatory foods, treating gut infection, detoxing mold, rebalancing gut bacteria, and addressing nutrient deficiencies, stress, traumas, and previous head injuries.

Address traumas and stress

To heal your gut, you need to be in rest and digest mode. Traumas and unmanaged stress will keep you in the fight, flight, or freeze mode, which prevents the gut from fully healing [15]. This is why it’s essential to incorporate trauma healing and stress management into your gut healing program.

Remove and detox from mold

Almost 50% of homes nowadays have water damage [16]. Mold toxins will wreck your gut lining. This is why it’s important to remove and detox from mold if it’s a factor for you. 

Provides your body with gut-sealing nutrients

Vitamins A and D are two of the most important nutrients for gut and immune health. Test your vitamin D levels and work to reach optimal levels, which are 60 – 80 ng/mL (150 – 200 nmol/L) [17]. Increasing your intake of vitamin A and D foods, such as liver and egg yolks, and supplementing if necessary is important. Vitamins A and D work together. Also, thyroid hormones work with vitamin A, so it’s important to make sure you have healthy vitamin A levels.

L-glutamine is an amino acid that intestinal cells use as their primary energy source. There are high amounts in bone broth, and it can be supplemented as well. Increasing L-glutamine can help heal a leaky gut.

Common digestive issues with hypothyroidism and how you can address them

If you have the following digestive issues, it’s important to get your thyroid levels under control. Then, consider these tips for relief and to maintain optimal digestion. 

Bloating/digestive discomfort

Low stomach acid, low digestive enzymes, Small Intestinal Bacterial Overgrowth (SIBO), poor gut movement, and dysbiosis in Hashimoto’s can contribute to bloating and digestive discomfort.

Aside from seeing a holistic provider to test and address the gut infections and dysbiosis, consider the following:

  • Betaine HCl (use code THYROIDSTRONG) to replenish stomach acidity
  • Full-spectrum digestive enzymes (use code THYROIDSTRONG), especially ones that digest bloat-inducing sugars and fibers
  • Digestive bitters to support gut movement
  • Probiotics to help support the gut flora
  • Avoiding trigger foods such as legumes (beans and lentils) and sugars
  • Activated charcoal to bind the gas

Indigestion and acid reflux

Acid reflux is when you feel that yucky sour burp or heartburn after meals, but it can also show up as chronic coughs or unexpected dental cavities. Many people, including some doctors, think acid reflux is due to too much stomach acid. However, too little acid can cause reflux as well [18]. 

Hypothyroidism is more likely to lower stomach acid and digestive enzyme production, along with slowed gut movement. These can all contribute to poor digestion and post-meal discomfort.

Aside from avoiding laying down right after eating, consider the following for relief:

  • Betaine HCl (use code THYROIDSTRONG) to replenish stomach acid
  • Digestive enzymes (use code THYROIDSTRONG) to replenish digestive enzymes
  • Digestive bitters before meals to stimulate gut movement and bile flow
  • Probiotics to support the gut flora balance
  • Avoiding trigger foods such as acidic foods and fatty meals, especially at night

Key insight #3: Hypothyroidism can lead to digestive problems such as bloating, indigestion, acid reflux, irritable bowel syndrome, constipation, and gallbladder problems.


Hypothyroidism can slow gut movement, causing constipation. So, you want to ensure you get at least 30 grams of fiber every day and drink enough water, around 8 – 10 glasses a day. 

If hard stools are a problem for you, certain magnesium supplements such as magnesium citrate and oxide can help loosen the stool. It’s also beneficial to supplement with some magnesium daily since our food chain is low in magnesium. I recommend this magnesium (use code THYROIDSTRONG).

See also Small Intestine Bacterial Overgrowth below.


Because hypothyroidism slows down cholesterol metabolism in the liver and bile duct secretion, gallbladder problems are very common in hypothyroid patients [19]. Bile typically makes your stool brown, so if your stool is consistently light-colored, your gallbladder might be under-functioning.

Before I got my Hashimoto’s under control, I used to get excruciating gallbladder attacks twice a month that would land me in the ER at least 4 times a year. The pain was so bad they’d give me morphine and recommend getting my gallbladder removed. The ultrasound showed chronic gallbladder inflammation and sludge. 

The decision to remove your gallbladder or keep trying natural options is very personal and should be between you and your doctor. I’m glad I managed to keep mine. These gallbladder attacks are now a thing of the past once I learned how to better manage Hashimoto’s by:

  1. Eating an anti-inflammatory diet.
  2. Maintaining healthy cholesterol levels, because cholesterol is a key component of bile.
  3. Increasing fatty fish consumption or supplementing with fish oil may improve gallstones by improving your blood lipids [20].
  4. Removing gluten. Many Hashimoto’s women also have gluten sensitivity or Celiac disease, which also correlates with recurrent gallbladder inflammation [21]. For me, getting rid of gluten made a big difference.
  5. Ensuring adequate fruit and vegetable intake, at least about 8 servings per day (~1 cup raw or ½ cup cooked per serving). This helps balance inflammation and these contain magnesium, which may be a risk factor for gallstones when deficient [22].
  6. These digestive enzymes may also help, though I don’t need them to manage my gallbladder issues anymore. 

Small intestine bacterial overgrowth

Due to slowed gut movement, suboptimal bile flow, and low stomach acid, small intestine bacterial overgrowth (SIBO) is more common among Hashimoto’s patients [23]. 

SIBO is when gut bacteria overgrow in your intestine when they should be in your colon. These bacteria can then ferment your food, causing:

  • Bloating, especially in lower-middle third of your belly
  • Gas 
  • Acid reflux
  • Stomach pain and other digestive distress
  • IBS and digestive irregularity and other symptoms. 

SIBO can also cause leaky gut, inflammation, and nutrient deficiencies. It’s also linked to many non-digestive symptoms such as fibromyalgia, anxiety, and depression [24,25]. 

SIBO is a controversial diagnosis because studies are mixed and in some cases treating it doesn’t improve the symptoms [26]. Some people respond well to probiotics and fiber as a SIBO treatment, while others do better with a low FODMAPs diet, antibiotics, and herbs that stimulate gut movement. This is why it’s crucial to see a practitioner and get personalized advice. 

Key insight #4 Many supplements like digestive enzymes, betaine HCl, and probiotics can relieve common digestive problems. However, addressing the root causes and optimizing your thyroid hormones are also key.

Note: The supplements mentioned here can all interact with your medications or may not be right for you, so it’s important to check with your doctor before introducing any supplements.


A leaky gut is a major contributor to Hashimoto’s and digestive problems that many Hashimoto’s patients struggle with. Allowing a leaky gut to continue will only make things worse. The good news is that:

  1. You’re not alone.
  2. It’s possible to heal your gut and re-optimize your digestion naturally.

Thyroid Strong is a personalized self-care program to help you take control of Hashimoto’s and get in shape. Aside from my optimized exercise program, there are also 20 hours of bonus content with functional medicine doctors diving deep into these root contributors of Hashimoto’s. Join the Thyroid Strong community today and take back your health.

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Article's References

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