Healthy Hormones

The Best Hashimoto’s Thyroiditis Natural Treatments

What are some Hashimoto's thyroiditis natural treatments?

What can you do to get rid of many of the symptoms of Hashimoto's or even possibly make it go away altogether?

In this article, I will walk you through the most effective natural treatments for Hashimoto's.

This will include common nutrient deficiencies that are present in Hashimoto's and the supplements you should consider using.

I will also discuss the most common food sensitivities and dietary recommendations for Hashimoto's.

Finally, I will touch on infections and toxins that may trigger or worsen Hashimoto's.

Let's get started...


Consider Nutrient Deficiencies

Many nutrients are essential for normal thyroid and immune system function. A deficiency of them sets a person up for the development of conditions such as Hashimoto's and other autoimmune diseases.

In our affluent society where there is generally no lack of food availability, how could anyone be deficient in nutrition? That doesn't seem possible.

Several things play a role (taken from Hashimoto's Thyroiditis Root Cause by Izabella Wentz):

  • Modern farming techniques - Non-organic farming typically involved using fertilizers and pesticides. Also, a typical field is used year after year to plant the same crop, which will deplete the soil of nutrients.
  • Standard American Diet - The typical diet eaten by most Americans contains highly processed, nutrient-deficient food.
  • Medications - Millions of people take medications on a daily basis that affect the absorption of nutrients in the gut and alter the beneficial bacteria in our digestive system that are essential for normal digestion of food. These include acid blockers (omeprazole, ranitidine, etc.), antibiotics, and even oral birth control pills.
  • Food Sensitivities - Many people are sensitive to certain foods and may not even know it. The most common are dairy and gluten. These sensitivities cause an increase in inflammation of the digestive tract which can affect it's ability to absorb nutrients.
  • Hidden Infections - Patients may have infections they don't even know they have. These include H. pylori, intestinal parasites, etc. All can increase inflammation and alter the normal gut flora which can impair nutrient absorption.
  • Restrictive Diets - Diets that are not nutritionally balanced can do more harm than good.
  • Hypothyroidism - Yes, being hypothyroid can itself cause nutrient deficiency by slowing the emptying of the stomach, reducing the amount of acid in the stomach, and even causing an imbalance of gut bacteria.

Common Nutrient Deficiencies in Hashimoto's


Studies have shown that low levels of selenium can serve as a trigger for the development of Hashimoto's.

You can become deficient because of gut issues (inflammation, altered gut flora) or even from gluten-free diets.

Symptoms of selenium deficiency include anxiety and hair loss.

Taking selenium will reduce thyroid antibody levels and anxiety symptoms.

Studies have shown that selenium supplementation is helpful even if the selenium levels are normal.

How to Supplement with Selenium

Why I Like It

May reduce antibodies in patients with Hashimoto's

Also acts as an  anti-inflammatory

May help reduce anxiety symptoms

Helps boost T4 to T3 conversion (helpful in those with high reverse T3)

Who Should Use It

    • Patients with hair loss or hair thinning
    • Patients with a known thyroid disorder and hair loss
    • Patients with other nutrient deficiencies like zinc or iodine
    • Patients who frequently take acid blockers for acid reflux
    • Patients with other GI related issues (IBS, gas/bloating, IBD)
    • Patients also taking zinc

How to Use

    • Take 200-400 mcg per day (do not exceed 400 mcg daily)

My Recommended Brand and Product


Ferritin is the iron storage protein. It is essential for transporting thyroid hormone into the cells.

Lack of ferritin causes hair loss, fatigue, cold intolerance, and shortness of breath.

Ferritin levels should be checked in all Hashimoto's patients, especially those that are experiencing hair loss.

The optimal ferritin level for thyroid function is 90-110 ng/ml.

Iron levels can best be restored by eating foods high in iron such as meats, especially organ meats. Vitamin C also helps with iron absorption.

Sometimes, supplementation may be necessary at least for awhile.

How to Supplement with Iron

Why I Like It

May boost energy levels

Up to 50% of Hypothyroid patients are deficient in iron

Helps promote thyroid conversion & function

Generally works within 1-2 months

How to Tell if You Need It

Check your iron studies and only supplement if your levels are sub optimal or low:

  • Ferritin - Optimal Levels = 40-50
  • Serum Iron - Middle of the reference range
  • TIBC (Total Iron Binding Capacity) - Middle of the reference range
  • Percent Saturation - 35-38%

How to Use

  • Liquid Iron:  start with 10 ml each day, do not exceed 20 ml per day (if you take more than 1 dose per day make sure to split it apart from one another and take at least 4 hours away from your thyroid medication)
  • Iron Capsules:  start with 1 capsule of iron and increase up to 3 per day as tolerated and based on your serum iron/ferritin levels (take at least 4 hours away from your thyroid medication)

My Recommended Brand and Product

Use liquid iron if you have intestinal issues such as gas, bloating, diarrhea, constipation or if you have previously failed capsule forms of iron:

Use this capsule form if you don't tolerate the liquid iron version above (some patients have various symptoms on liquid iron such as teeth pain or simply can't tolerate the taste or texture of the liquid):

B Vitamins

B vitamins are commonly deficient in Hashimoto's patients, especially B12.

This is due primarily to low stomach acid which is common in Hashimoto's.

Signs and symptoms of deficiency include fatigue, grooves in your tongue, and an elevated homocysteine level (which should be less than 6 umol/L.

All Hashimoto's patients should have their B12 level checked.  If it is <1000, they should consider supplementing.

By the way, over 60% of the population has a gene mutation in the enzyme MTHFR, which can impair the body's ability to metabolize B vitamins. This can cause the homocysteine level to become elevated, which is a risk factor heart disease and other conditions.

It is important for these patients to take a methylated form of B vitamins, especially folic acid. If you don't know if you have the gene mutation, either get tested or take a methylated B vitamin. My recommended brand can be found here.

You should also consider supplementing with B12 shots.

Many Hashimoto's patients have GI issues that can impair the absorption of nutrients.

Completely bypassing the GI tract by giving it in shot form is the best way to ensure that the B12 is absorbed as much as possible.

How to Supplement with B12 Shots

Why I Like It

May boost energy and reduce fatigue

May help increase metabolism and fat loss

Help improve mood and increase concentration

Generally works within 1-2 weeks

How to Tell if You Need It

Patients with the following symptoms should consider using B12 shots:

    • Obesity or weight gain
    • Fatigue or low energy levels
    • Lack of sleep or insomnia
    • Depression or anxiety
    • Hair loss or lack of hair growth
    • Serum B12 levels < 1000
    • Homocysteine levels > 9
    • MCV (mean corpuscular volume) > 92
    • High levels of inflammation

How to Use

    • Take 5,000 mcg of Methylcobalamin every 7 days for at least 10 weeks
    • You will need 10 weeks worth of injections to saturate tissues and increase cellular B12 levels

My Recommended Brand and Product

Make sure you get methylcobalamin shots in a high enough dosage for best results.


Zinc is essential for normal thyroid function. Most patients with thyroid disease are deficient.

Zinc is not stored in the body, so a consistent daily intake is required to maintain levels.

Zinc deficiency can be detected by a low alkaline phosphatase level, which is a routine lab tests run by most labs. It's optimal range should be 70-90 U/L.

How to Supplement with Zinc

Why I Like It

Many people are deficient in zinc

May help with T4 to T3 conversion

May increase cellular sensitivity to thyroid hormone

Has anti-inflammatory effects

How to Tell if You Need It

    • If you have Hashimoto's and hair loss
    • If alkaline phosphatase is < 70

How to Use

    • Take 30-60 mg daily (do not take more than 60 mg)

My Recommended Brand and Product

Vitamin D

Vitamin D is essential for normal thyroid function.

Studies show that over 40% of the population is deficient. However, that study defined deficiency as a 25-hydroxy vitamin D level of less than 20 ng/ml. Other studies show that a level of 60-80 ng/ml is needed for optimal thyroid function. When using those levels as "normal," over 90% of the population is deficient.

Low levels of vitamin D have been shown to increase the risk for development of Hashimoto's.

All Hashimoto's patients should have their 25-hydroxy vitamin D level checked yearly.

Most patients need at least 5000u per day of vitamin D3 with K2 such as this one.

How to Supplement with Vitamin D3

Why I Like It

Most people are deficient in Vitamin D

May help with T4 to T3 conversion

Deficiency increases risk for Hashimoto's

Has over 200 functions in the body

How to Tell if You Need It

    • 25-hydroxyvitamin D level < 50

How to Use

    • If < 40 take 10,000u daily for 90 days, then drop to 5000u daily.
    • If > 40, take 5000u daily
    • Check level yearly

My Recommended Brand and Product


Iodine can be listed under both toxins and essential nutrients for normal thyroid function.

That's because a deficiency of iodine is the world's leading cause of hypothyroidism.

However, excessive amounts of iodine can increase the risk of the development of Hashimoto's.

This means iodine has a small therapeutic window - Too little is bad, but too much is also bad.

Hashimoto's was rarely seen in the United States until the nationwide salt iodinization program began in 1924.

Some people fear that using iodine in patients with Hashimoto's may make the condition worse, and it can - but usually only in patients with other thyroid issues and those on medications that are known to interfere with thyroid function (lithium, amiodarone, etc.).

In the majority of cases, and if used correctly, iodine can be safe to use in patients with both hypothyroidism and Hashimoto's.

Taking the iodine with selenium can help prevent any negative effects - such as an increase in thyroid antibodies that has been shown to occur in some studies.

Supplementing with both selenium and iodine has been shown to reduce TSH and result in an increase in peripheral thyroid hormones and may protect against an increase in thyroid antibodies in patients.

Patients with thyroid issues like Hashimoto's usually tolerate iodine, but it must be accompanied with normal and optimal selenium and iron levels.

If you decide to take iodine, make sure your thyroid antibodies are checked regularly by an experienced provider.

How to Supplement with Iodine

Why I Like It

May improve thyroid function

May help detox some substances

If deficient with improve other systemic problems

Generally works very quickly in deficient patients

Who Should Use It

Supplementing with iodine can be difficult.

If possible I recommend testing your urinary excretion of iodine prior to supplementation.  If you decide not to test yourself then start out at very low doses (~200-300mcg per day) and slowly increase the dose based on your symptoms.

How to Use

    • Take 200-300 mcg per day and slowly titrate dose based off of symptoms - discontinue if you experience any negative side effects and seek professional help
    • It is safest to take it with selenium 200-400 mcg daily

My Recommended Brand and Product

For low doses start with 200-300 mcg of kelp caps and titrate your dose as tolerated:

For higher doses I recommend liquid iodine with a combinations of both iodine and iodide:

Look For Food Sensitivities

So, what foods should you eat? What foods should you avoid?


Everyone by now how has heard about this mysterious gluten molecule that seems more dangerous than a nuclear weapon. Why is it so bad?

Multiple studies such as this one have shown a strong link between Hashimoto's and gluten intolerance.

There is a higher incidence of Celiac Disease in Hashimoto's patients. However, even people that test negative for gluten antibodies can still react to it.

Some researchers estimate that up to 1/3 of the population has some degree of gluten sensitivity.

It is believed that gluten looks similar to parts of the thyroid gland. This causes the immune system to make antibodies against the thyroid because of molecular mimicry like I discuss under Consider Infections below.

Gluten also worsens intestinal permiability (leaky gut).

Gluten is a component of wheat, so it is present in pasta, breads, crackers, etc. Gluten is also frequently used as a filler in other foods and is commonly found in things such as shampoo, makeup, etc. It is even present in some medications!

The most simple and cost-effective way of determining if you are gluten sensitive is using an elimination diet. In other words, remove it completely from your diet for about 3 weeks. After the 3 weeks are over, re-introduce it into your diet. If you have any kind of reaction - nausea, diarrhea, dizziness, fatigue, etc. - you are most likely gluten sensitive.

To top it off, the immune response to gluten can last for up to 6 months after eating it!

That is why it is critical to follow a gluten-free diet 100%. Anything less may not reduce the thyroid inflammation adequately to prevent the Hashimoto's from killing it.

There is enough data for me to feel confident in recommending a gluten-free diet in all Hashimoto's patients.

Actually, I believe there is ample evidence to suggest that everyone should be gluten-free.

This has fortunately gained enough traction in society that becoming gluten-free is much easier than it was just a few years ago.

A quick internet search will uncover multiple websites with recipes and other information to help you in this journey. Many grocery stores also have sections featuring gluten-free products.

If you want to read more about gluten, I highly recommend the book Wheat Belly by Dr. William Davis.

By the way, removing gluten from my diet was the single most effective therapy that brought me back to a life of health.

Other Food Sensitivies

About 90% of food sensitivities occur from the following foods:

  • Wheat
  • Milk
  • Soy
  • Eggs
  • Peanuts
  • Tree nuts
  • Shellfish
  • Fish

Tomatoes, potatoes, peppers, corn, citrus, beef and pork can also cause problems in some people.

Your doctor can order a basic food allergy panel which will check most of these common food allergies. If you test positive, you know that you need to remove that food from your diet.

Remember, however, that you may still be sensitive to that food even if you don't have antibodies to it.

There are also tests available to check for IgG antibody levels to various foods.

As I discussed under gluten, the most simple way for you to find out if you have any food sensitivities is to use the elimination diet.

You can either remove one food at a time for 3 weeks, then reintroduce it and see if you react. This process could take 6 months or more to get through all of the foods. Or, you can bite the bullet and remove all of the top 8 culprits together for 3 weeks, then reintroduce each one separately every few days. If you react, keep that food out of your diet. If you don't react, you can continue to eat it then reintroduce the next one on the list.

Get On An Anti-inflammatory Diet

The goal for Hashimoto's is to reduce the level of inflammation in the body, especially the thyroid.

One of the best ways of accomplishing that goal is to remove inflammatory foods.

The Most Inflammatory Foods

  1. Gluten
  2. Sugar
  3. Dairy
  4. Vegetable oils
  5. Artificial sweeteners and preservatives
  6. Saturated fats

Removing these things from your diet will have a HUGE impact on your health, including your thyroid health.

There are several popular diets that are excellent at removing these things and giving you instruction on what you can eat.

The best diets for Hashimoto's are:

Any of these diets will have you eating clean, whole foods and reducing your systemic inflammation quickly.

It can take several months for the inflammation to reduce substantially, so don't give up!

Remember, even though you start one of these diets, you may still need to do an elimination diet to help you determine what food sensitivities you have.

Get Your Gut Healthy

1.  Betaine HCL with Pepsin

Advertisements from pharmaceutical companies make it seem like almost everyone has too much stomach acid.

In reality, it's exactly the opposite.

Most patients have low levels of stomach acid.  That includes almost all Hashimoto's patients.

When stomach acid is low we can't absorb nutrients as well.

The lack of acidity also makes it easier for bacteria and other organisms to survive their passage through the stomach and set up residence somewhere in the body, causing an infection to develop.

Adding betaine hcl with pepsin can help increase the stomach acid to optimal levels and relieve many of the reflux and other GI symptoms you may be having.

Betaine HCl and Pepsin should be taken after a protein-rich meal, starting with one capsule per meal, at the end of the meal. The dose should be increased by one more capsule at each meal until symptoms of too much acid are felt (burping, burning, warming in the stomach region, etc.). At that point, you will know that your dose is one capsule less than what resulted in symptoms.

If you get burning after taking it, drinking a mixture of one teaspoon of baking soda in a glass of water will reduce these temporary symptoms.

Don't take betaine hcl is you have a history of ulcers or if you are taking an NSAID or steroid medication.

My favorite brand of Betaine hcl with Pepsin is this one.

2.  Probiotics

Most hypothyroid and Hashimoto's patients have some degree of intestinal dysbiosis (usually due to decreased kinetic movement of the bowels from lack of thyroid hormone).

As a result many Hypothyroid patients are prone to develop a condition known as Small Intestinal Bowel Overgrowth (or SIBO).

Patients with SIBO tend to get gas and bloating with lactobacilli-based probiotics but can usually tolerate soil-based probiotics well.

That's why it's usually best for most Hashimoto's patients to use a good soil-based probiotic such as this one.

Consider Infections

Various infections have been implicated in the development of autoimmune diseases, including Hashimoto's.

There are 2 main theories of how these infections trigger the immune system to attack the thyroid gland.

  1. Molecular Mimicry - In this theory, bacterial cells or other microbes look very similar to cells within our body (such as thyroid cells). Our immune system produces antibodies to kill the microbes, but since they look like our own cells, the end result is the antibodies produced attack the cells in our body instead of just the microbes.
  2. Bystander Effect - Another theory suggests that the microbes (especially viruses) take up residence in the cells of our body. In the process of killing the microbes, our immune system also damages the cells in our body where the viruses are residing.

The most common organisms associated with Hashimoto's are Mycoplasma, Candida, and Epstein-Barr virus.

Other organisms implicated include Helicobacter pylori, Lyme disease, Yersinia, Coxsackie virus, and Hepatitis C. Intestinal parasites may also be present.

Low stomach acid, nutrient deficiencies, altered gut bacteria, and an impaired immune system all contribute to Hashimoto's patients having an increased risk of having any of these infections.

If you aren't improving despite following a strict diet and restoring any nutrient deficiencies that are present, that is the time to start looking for hidden infections or toxins.

Avoid Toxins

Unfortunately, our world is full of chemicals and other substances that can be harmful to us, including our thyroid gland.

An example of these are the endocrine disruptor chemicals (EDC). They are everywhere and are impossible to completely avoid.

Some types of them are even stored in the fat calls of our body. This is bad because if we start burning fat as an energy source (which happens in the diets listed above), many of these stored chemicals are released. They can worsen thyroid function and stop weight loss.

An example of an EDC that is controversial is fluoride. It has been added to many water supplies since the 1940s because it reduces the incidence of tooth decay. However, fluoride can be toxic to thyroid cells and can cause inflammation and even thyroid cell death.

There are a few common sense things that we all can do to at least reduce the amount of exposure to endocrine disruptor chemicals:

  • Drink filtered water
  • Drink from glass or metal containers (avoid plastic bottles)
  • Install a shower head filter such as this one.
  • Use a non-fluoride toothpaste.
  • Avoid using herbicides on your lawn or plants (Google "Homemade Weed Killer" for safe alternatives).

You can also help your body get rid of toxins by doing one simple thing - Sweat!

Sweating is one of our body's best detox mechanisms.

Regular time in a sauna and high intensity interval training (HIIT) are 2 excellent ways of activating our sweat function.


There are several natural treatments that you can do to improve your Hashimoto's symptoms.

Considering potential nutrient deficiences and taking targeted, high-quality supplements is critical.

It is also very important to identify any food sensitivities that you may have by utilizing the elimination diet.

Increasing your stomach acid and taking a good probiotic can help to increase nutrient absorption and improve your immune system.

Infections and toxins can also be playing a role in your autoimmune condition.

Now it's your turn.

Are you appropriately supplementing for any deficient nutrients?

Do you have any food sensitivities?

Have you identified any infections or toxins that may be worsening your Hashimoto's?

Leave your comments below!

About the Author Dr. Jeff Whelchel

Dr. Whelchel is a family physician who specializes in functional medicine, especially hormone optimization. He has over 20 years experience in private practice managing patients with various medical issues. His passion is helping patients reach their full potential of wellness and quality of life. He grew up in the Texas Panhandle where he currently lives. He is married and has 3 awesome children.

Leave a Comment:

Solmaz says July 3, 2021

Hi Dr. Welchel, In 2018, I was diagnosed with P.G. In Dec. 2019 I was hospitalized for a very bad covid. Recently, my T-4 level dropped to below normal level but my TSH is within normal range. My thyroid has had benign nodules since 2010. I have many symptoms that match with possibly Hashimoto’s
Can you please email me so I could make an appointment to speak with you.
Thank you.

    Dr. Jeff Whelchel says July 17, 2021

    Hello. I am only seeing patients in person in my office that live in Texas. Many states have gotten very strict about whether you can take care of residents from their states if you aren’t licensed in that state.. If you live in Texas, please call my office using the number listed in the “Contact” tab.

Kellyann says July 13, 2021

Thank you for the information in this article.I found it extremely helpful!

    Dr. Jeff Whelchel says July 17, 2021

    Thank you, Kellyann. I’m glad it was helpful for you.

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