Thyroid Strong

What are the differences between hypothyroidism and Hashimoto’s?

by | Mar 7, 2023 | Symptoms

The current standard of care diagnoses and treats hypothyroidism and Hashimoto’s the same. This explains why so many women still have symptoms even when their lab tests are normal

In countries that fortify their salts with iodine, most cases of hypothyroidism are autoimmune in nature, including Hashimoto’s, atrophic thyroiditis, and Graves (which can swing between high and low thyroid functions). These types of hypothyroidism arise from inflammation and your immune system attacking your thyroid. In this article, I’ll cover: 

  • The key differences between hypothyroidism and Hashimoto’s 
  • How to address the root causes of inflammation and autoimmunity so you can thrive despite the diagnosis.

What is the difference between hypothyroidism and Hashimoto’s?

In short, Hashimoto’s is a type of hypothyroidism caused by an autoimmune attack in your thyroid. Hashimoto’s remains the most common type of hypothyroidism in the US, accounting for ~80 – 90% of hypothyroidism cases. 

Hypothyroidism, or underactive thyroid, is a condition in which your thyroid glands do not make enough thyroid hormones to meet your body’s needs [1].

Hypothyroidism and Hashimoto’s?

Diagram: The Thyroid Axis and Different places in the body where hypothyroidism can start from, including the hypothalamus or pituitary gland in the brain, and the thyroid gland itself.

There are three types of hypothyroidism:

  1. Primary hypothyroidism: the thyroid gland itself doesn’t function properly and doesn’t produce enough thyroid hormones
  2. Secondary hypothyroidism: the thyroid gland is working just fine, but the pituitary gland doesn’t produce enough thyroid stimulating hormone (TSH) to stimulate the thyroid
  3. Tertiary hypothyroidism: the problem lies with the hypothalamus gland in the brain, which signals the pituitary gland.

Key insight #1: Different types of hypothyroidism start in different places in your body. Often, the treatment and management will be different, too.

Depending on where the problem or damage occurs within the three layers of communication, the causes of hypothyroidism can vary.  

The major causes of hypothyroidism include (from the most common to the least common) [2]:

  1. Autoimmunity
  2. Surgical removal of part or all of the thyroid gland
  3. Radiation treatment
  4. Congenital hypothyroidism
  5. Thyroiditis (inflammation of the thyroid)
  6. Medications
  7. Too much or too little iodine
  8. Damage to the pituitary gland
  9. Rare disorders that infiltrate the thyroid

Are the symptoms of hypothyroidism and Hashimoto’s different?

Symptoms of hypothyroidism can vary from person to person, but common symptoms include [3]:

In Hashimoto’s disease, because your immune system attacks the thyroid, the thyroid gland becomes inflamed. There’s also more inflammation involved in the overall presentation of symptoms, which can show up as joint or muscle pain and hypermobility.

Many Hashimoto’s patients also develop another autoimmune disease. The risk increases significantly after being diagnosed with one autoimmune condition, of then being diagnosed with a second autoimmune condition. In some cases, some people may get an enlarged thyroid (goiter) due to the inflammation in the thyroid gland.

thyroid statistics for hashimoto's

Is Hashimoto’s disease diagnosed and treated differently than hypothyroidism?

In conventional medicine, both Hashimoto’s and hypothyroidism are diagnosed and treated the same way. Your doctor will typically screen for hypothyroidism by testing TSH and, in some cases, T4. If the numbers come back out of range, they will typically prescribe levothyroxine or a T4 hormone replacement as first-line therapy [4].

It can take a few weeks or months to get to the right dosage where your lab tests are stable and in-range. To them, it does not matter whether you have autoimmunity or inflammation or not.

Whereas, in naturopathic and functional medicine, your doctor will seek to distinguish between Hashimoto’s and hypothyroidism. The root causes are very different, so these two conditions require different treatments.

In Hashimoto’s disease, because your immune system attacks the thyroid, the thyroid gland becomes inflamed. There’s also more inflammation involved in the overall presentation of symptoms, which can show up as joint or muscle pain and hypermobility.

Many Hashimoto’s patients also develop another autoimmune disease. In some cases, some people may get an enlarged thyroid (goiter) due to the inflammation in the thyroid gland.

Key insight #2: Hashimoto’s is a type of Hypothyroidism, caused by inflammation and autoimmune attacks on the thyroid. Conventional medicine treats all types of hypothyroidism the same way, by replacing thyroid hormones. However, many Hashimoto’s patients still feel symptoms and only get better once they start addressing the root causes of autoimmunity and inflammation.
In many cases, Hashimoto’s patients will need both thyroid medication from a conventional doctor and the following support from a naturopathic or functional medicine doctor. It’s both, not either or, and you’ll likely need both if the autoimmune attacks have destroyed enough thyroid tissues. In some states, naturopathic doctors can prescribe thyroid hormones or desiccated thyroid supplements.

Testing the full thyroid panel, even with normal TSH

For most medical doctors, the thyroid stimulating hormone (TSH) is the first and sometimes the only test ordered.  But a full thyroid panel will often reveal more and will help to diagnose subclinical thyroid conditions with a normal TSH, which are often missed.  

The full thyroid panel includes:

  • TSH – The measurement of thyroid stimulating hormone (TSH) in the blood.
  • Free and bound thyroid hormones 
    • Free T3 – The measurement of T3 that is floating free in the blood. T3 is the active form of thyroid that has an effect on your cells.
    • Free T4 – The measurement of T4 that is floating free in the blood. T4 is the inactive form of thyroid and is converted to T3 in your tissues.
    • Total T3 – The measurement of both free T3 and T3 bound to other proteins in the blood.
    • Total T4 – The measurement of both free T4 and T4 bound to other proteins in the blood.
  • Thyroid antibodies
    • Thyroid peroxidase (TPO) antibody – This tests for the presence of antibodies against the TPO enzyme in the blood. TPO is an enzyme that is used for production of the thyroid hormones. It can be elevated when you have either Hashimoto’s or Grave’s disease.
    • Thyroglobulin (TG) antibody – Thyroglobulin is a protein and is the storage form of the thyroid hormone within the cells of the thyroid. This test measures for the presence of antibodies against the TG protein. It can be elevated when you have either Hashimoto’s or Grave’s disease.
  • Reverse T3 (RT3)  – Reverse T3 is an inactive form of the T3 hormone. It can block the conversion of T4 to T3.

For example, a patient with subclinical hypothyroidism could have a normal TSH, but lower than optimal levels of Free T3 and Free T4. And if they have elevated antibodies, they could have Hashimoto’s or be at risk of developing Hashimoto’s in the near future.

To learn more about each test in the thyroid panel, and their normal and optimal ranges, check out our normal vs optimal thyroid labs post.

Addressing root causes of chronic inflammation and working to put you into remission

When the thyroid antibodies are elevated, this tells us two things. 

  1.  The root cause of your hypothyroidism is due to autoimmunity, or your immune system attacking itself.
  2. The level of the antibodies tells us how much inflammation there is. The higher the antibody, the more inflammation there is and the worse your symptoms tend to be.   

Based on this information, your doctor will treat Hashimoto’s differently to try to lower the antibodies and thus the inflammation in an effort to put you into remission.

Supplementing iodine only when indicated

Another aspect that’s often confusing is whether iodine supplementation is helpful or not for hypothyroidism.  Again, this depends on the root cause.

For instance, if you have an iodine deficiency, you will have hypothyroidism because you lack a key building block to make the thyroid hormones. You need 3 atoms of iodine to make T3 and four atoms to make T4. In this case iodine supplementation will be beneficial. This type of iodine deficiency is much more common in developing countries that don’t add iodine to their salt.

Key Insight #3: Knowing whether you have Hashimoto’s vs other types of hypothyroidism can make a big difference. For example, iodine supplement, and eating food or salt high in iodine can be bad for Hashimoto’s. By better managing inflammation, you may be able to stop further autoimmune attacks on your thyroid or prevent more autoimmune diseases from developing.

Whereas, in many cases of autoimmunity without an iodine deficiency, supplementing with iodine can be harmful and may even trigger flares.

Stopping further destruction of the thyroid glands and minimize the risk of other autoimmune diseases

To treat the root cause, you aim to lower the inflammation to reduce the antibodies and stop further destruction of the thyroid glands.  

When you have an autoimmune condition, it often leads to another one. Once your immune system is already haywire and self-attacking, it is a lot more likely to start attacking something else in your body.  Common comorbid autoimmune conditions with Hashimoto’s include rheumatoid arthritis (RA), psoriatic arthritis, Sjögren syndrome (SS), celiac disease, and type 1 diabetes [5].  

Shooting for optimal health, metabolism, and energy, not just optimal labs

Many Hashimoto’s ladies come to me feeling symptoms because their doctors only titrated their medications until their labs are normal. This is where root cause medicine can come in and fill the gaps by treating the whole person. 

By addressing your inflammation through diet, exercise, and other lifestyle changes you can put your Hashimoto’s into remission. This means you have minimal antibodies, optimal thyroid hormone levels, and no bothersome symptoms. The goal of your treatment should be to thrive with optimal health, metabolism, and energy. 

Considering prevention rather than treatment

If you knew that you could stop Hashimoto’s years before it appears, would you rather prevent it? 

If you’re reading this, odds are you’ve been diagnosed already. But you will have family members and friends with increased risk factors for Hashimoto’s. It’s not a disease that develops overnight, but rather comes on slowly [6]. Many people also felt some symptoms for years or decades before they’re finally diagnosed. 

If you have the following risk factors [7], consider getting full thyroid panels regularly to see if you have antibodies or suboptimal thyroid hormone levels. 

  • Female
  • Had a baby in the past 12 months or menopause
  • Have had other thyroid problems, or thyroid surgery
  • Have been exposed to radiation, whether through environmental, work, or as a medical treatment
  • Thyroid issues, especially Hashimoto’s, run in the family
  • Have another autoimmune disease, such as celiac, pernicious anemia, and rheumatoid arthritis


If you’ve been diagnosed with hypothyroidism, it’s a good idea to ask your doctor if it could also be Hashimoto’s. While 0.3% of Americans ages 12 years and older have overt hypothyroidism and 4.3% have subclinical hypothyroidism [8], 1-2% of people in the US have Hashimoto’s [9]. 

Since Hashimoto’s is the most common cause of hypothyroidism in the United States, it’s estimated that more than 14 million Americans are affected [10] and the incidence is estimated to be 3.5 per 1000 women per year and 0.8 per 1000 men per year [11].

If you do have Hashimoto’s it’s a good idea to see a naturopathic or functional medicine doctor who can guide you through addressing the root causes and putting your Hashimoto’s into remission.

Thriving and losing weight with Hashimoto’s involve much more than diet and exercise. So, I created Thyroid Strong to be a comprehensive program. It includes both exercise programs and over 20 hours of content from functional medicine doctors and health experts.

It’s based on a decade of research, and trial and error I did to put my Hashimoto’s into remission, including what labs to ask for. That way you can be a self-advocate. No other program out there includes both exercise and functional medicine pieces.


Article's References

1 (2013) Hypothyroidism. Endocrine System, National Library of Medicine.

2 (2015, September 9) Hypothyroidism. American Thyroid Association.

3 (2022, November 15) Hypothyroidism (underactive thyroid). National Institute of Diabetes and Digestive and Kidney Diseases, NIDDK | National Institute of Diabetes and Digestive and Kidney Diseases.

4 Underactive thyroid (hypothyroidism) – Diagnosis.

5 Ruggeri, R. M., Trimarchi, F., Giuffrida, G., Certo, R., Cama, E., Campennì, A., Alibrandi, A., De Luca, F. and Wasniewska, M. (2017) Autoimmune comorbidities in Hashimoto’s thyroiditis: different patterns of association in adulthood and childhood/adolescence. Eur. J. Endocrinol. 176, 133–141.

6 (2016, March 29) Hashimoto’s thyroiditis. American Thyroid Association.

7 (2013) Hypothyroidism. Endocrine System, National Library of Medicine.

8 Patil, N., Rehman, A. and Jialal, I. (2022) Hypothyroidism, StatPearls Publishing.

9 Mincer, D. L. and Jialal, I. (2017) Hashimoto thyroiditis,

10 Dolan, K., Finley, H., Gasta, M. and Houseman, S. (2018) Managing Hashimoto’s Thyroiditis Through Personalized Care: A Case Report. Altern. Ther. Health Med. 24, 56–61.

11 Mincer, D. L. and Jialal, I. (2022) Hashimoto Thyroiditis, StatPearls Publishing.

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