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Treatment Differences for Hashimoto’s and Hypothyroidism

Learn about how treatment options may differ between Hashimoto’s and hypothyroidism.
Treatment Differences for Hashimoto’s and Hypothyroidism
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Did you know that Hashimoto’s disease is the leading cause of hypothyroidism? While the exact number of those affected by Hashimoto’s is unknown, about 5 out of 100 Americans over 12 years of age old have hypothyroidism.

Regardless of the cause of hypothyroidism, those with hypothyroidism will likely seek treatment to help ease their symptoms. Since Hashimoto’s causes hypothyroidism, you may wonder if the treatment options for Hashimoto’s and hypothyroidism are the same.

In this article, we’ll explore the differences between Hashimoto’s and hypothyroidism, as well as treatment options.

Basics of hypothyroidism

Hypothyroidism is a general term that refers to an underactive thyroid. When you’re hypothyroid, your thyroid doesn’t produce enough essential thyroid hormones – T4 (thyroxine) and T3 (triiodothyronine) – to meet your body’s demands.

In the U.S., Hashimoto’s – an autoimmune disease – is the number one cause of hypothyroidism. Other causes of hypothyroidism include the following:

  • Thyroid cancer or surgery
  • Medication-induced
  • Radiation therapy

Although rare, some people are born with a missing or dysfunctional thyroid – this is known as congenital hypothyroidism.

What is the difference between Hashimoto’s and hypothyroidism?

Hashimoto’s is an autoimmune thyroid disorder, meaning your immune system attacks and destroys your thyroid cells. Due to this destruction, your thyroid gland can’t make enough thyroid hormone to meet your body’s needs. The result is an underactive thyroid gland (hypothyroidism). Hashimoto’s and hypothyroidism have the same set of symptoms, such as:

Diagnosing Hashimoto’s vs. hypothyroidism

Hypothyroidism is typically diagnosed based on your symptoms and your thyroid hormone levels. The best way to determine your thyroid function is through monitoring thyroid biomarkers via the following thyroid tests:

  • Thyroid-stimulating hormone (TSH) is a pituitary hormone that tells your thyroid to produce and release more thyroid hormone. The TSH test measures the amount of TSH in your blood. An elevated TSH level indicates hypothyroidism.
  • Free Thyroxine (Free T4) shows the available levels of T4 in your bloodstream. The majority of thyroid hormone secreted from your thyroid gland is in the form of T4. When measured along with TSH, your healthcare provider gets a good view of your thyroid’s function. A low free T4 level may indicate an underactive thyroid disorder.
  • Free Triiodothyronine (Free T3) measures the amount of T3, the active thyroid hormone, in your bloodstream.

Besides abnormalities in the above thyroid hormone levels, people with Hashimoto’s will almost always have evidence of thyroid autoimmunity, specifically elevated Thyroid Peroxidase (TPO) antibodies or thyroglobulin (TG) antibodies in the bloodstream.

The presence of thyroid antibodies in blood tests does not show how well your thyroid functions. Instead, it indicates an autoimmune disorder is likely present. It is possible to have thyroid antibodies in your blood but not have abnormal thyroid biomarkers or overt thyroid disease. Sometimes other autoimmune disorders, such as type 1 diabetes or rheumatoid arthritis, produce thyroid antibodies.

To recap, people with hypothyroidism typically have a high TSH with low free T4 and free T3 thyroid levels. People with Hashimoto’s test positive for thyroid antibodies and may have an elevated TSH with low free T4 and free T3 levels.

Free T3

Free T3 is a hormone produced by the thyroid gland. Levels of this fluctuate when individuals have an under or overactive thyroid gland.


Thyroid-stimulating hormone, TSH, is the hormone responsible for controlling hormone production by the thyroid gland. The hormone TSH is considered the most sensitive marker for screening for thyroid diseases and conditions. Our thyroid panel is ideal for TSH testing at home and will tell you how your levels compare to normal TSH levels.

TPO Antibodies

Thyroid peroxidase antibodies are antibodies that can bind to thyroid enzymes, suppressing thyroid function. They are elevated in a condition called Hashimoto's disease, which is the most common type of hypothyroidism in the USA.

Free T4

Free T4 is the predominant hormone produced by the thyroid gland. Levels fluctuate when individuals have an under or overactive thyroid gland. Testing your free T4 with this thyroid function test lets you see if your thyroid hormone production is at a normal level.

Reverse T3


RT3 is a metabolite of T4. Typically, when T4 loses an atom of iodine—a process known as monodeiodination—it becomes (T3), the active thyroid hormone.The body also converts T4 into rT3, which is an inactive form of T3 that is incapable of the metabolic activity that is normally carried out by T3.

Vitamin D


Some observational studies have found low blood levels of vitamin D in patients with hypothyroidism and Hashimoto’s as well as hyperthyroidism due to Gravesʼ disease. It is not clear from these studies if low vitamin D is a cause, a consequence or an innocent bystander in the development of these common thyroid conditions.

Are treatments for Hashimoto’s and hypothyroidism the same?

They can be. It all depends on the degree of hypothyroidism or Hashimoto’s.

Individuals with borderline or subclinical hypothyroidism may present with mild hypothyroidism symptoms. The TSH level may be slightly elevated, but T4 and T3 levels will be within normal limits. In contrast, those with overt hypothyroidism present with hypothyroidism symptoms and a marked increase in TSH with low free T4 and free T3 levels.

About 80% of those with subclinical hypothyroidism have thyroid antibodies. Despite the presence of thyroid antibodies, it doesn’t mean you have overt Hashimoto’s, though it is a risk factor. Just under 5% of those with TPO antibodies progress from subclinical to overt hypothyroidism. But when TPO antibodies are absent, less than 3% of patients go from subclinical overt hypothyroidism.


12 Week Hashimoto's
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What are the treatments for hypothyroidism and Hashimoto’s?

The treatment for those with overt hypothyroidism or Hashimoto’s is the same: thyroid hormone replacement therapy to optimize thyroid function. These medications replace your natural thyroid hormone when your body can’t produce enough, increasing levels to a normal range and optimal function. Replacing missing thyroid hormones can relieve symptoms of an underactive thyroid gland by allowing your cells to function correctly.

Both synthetic hormone and natural hormone treatments are available for hypothyroidism. The three thyroid medication options for the treatment of hypothyroidism include:

  • Levothyroxine (Synthroid, Levoxyl, Unithroid, Euthyrox, Tirosint): a synthetic version of the T4 hormone
  • Liothyronine (Cytomel): a synthetic form of the T3 hormone
  • Desiccated thyroid (Armour Thyroid, NP Thyroid): an animal-derived combination of natural T3 and T4

Treating subclinical hypothyroidism with thyroid replacement medication is controversial. Some providers may recommend treating it based on your symptoms and medical history, while others may recommend periodic monitoring without drug treatment.

Thyroid hormone replacement medications are generally not recommended for Hashimoto’s patients with TPO antibodies but normal thyroid biomarkers and no hypothyroidism symptoms. If lab values become abnormal or you develop symptoms, your healthcare provider may start exploring treatment options.

A note from Paloma Health

The best way to tell if Hashimoto’s autoimmune thyroid disease is the underlying cause of hypothyroidism is by checking for thyroid auto-antibodies. Our at-home testing kit makes diagnostic tests for TPO antibodies a cinch. All it requires is a finger prick blood sample to be mailed in. Not only will it test your TPO levels, but it will also report your TSH and free T4 and T3 levels giving you a complete picture of your thyroid function.

In addition to medication, Hashimoto’s and hypothyroidism patients also benefit from the comprehensive lifestyle approaches integrated into Paloma’s care philosophy, including:

  • Addressing any vitamin and nutritional deficiencies and imbalances
  • Incorporating anti-inflammatory and Autoimmune Protocol (AIP) principles into your diet
  • Prioritizing your sleep, maintaining hydration, getting physical activity, and managing stress levels

You can book an appointment with one of Paloma’s experienced thyroid health care providers, who will help you discuss a thyroid hormone replacement and lifestyle treatment plan to help ensure relief of your hypothyroid symptoms, optimal thyroid function, and overall wellness.

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Wartofsky L. Hashimoto’s Disease | NIDDK. National Institute of Diabetes and Digestive and Kidney Diseases. Published April 5, 2019. Accessed June 10, 2023

Hypothyroidism (Underactive Thyroid) | NIDDK. National Institute of Diabetes and Digestive and Kidney Diseases. Accessed June 10, 2023.

American Thyroid Association. Thyroid Function Tests | American Thyroid Association. American Thyroid Association. Published 2016. Accessed June 10, 2023.

Fröhlich E, Wahl R. Thyroid Autoimmunity: Role of Anti-thyroid Antibodies in Thyroid and Extra-Thyroidal Diseases. Frontiers in Immunology. 2017;8. doi:

Fatourechi V. Subclinical hypothyroidism: an update for primary care physicians. Mayo Clinic proceedings. 2009;84(1):65-71. doi:

Jonklaas J, Bianco AC, Bauer AJ, Burman KD, Cappola AR, Celi FS, et al. Guidelines for the treatment of hypothyroidism. Thyroid. 2014; 24(12): 1670 - 1751. doi:10.1089/thy.2014.0028


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Emilie White, PharmD

Clinical Pharmacist and Medical Blogger

Emilie White, PharmD is a clinical pharmacist with over a decade of providing direct patient care to those hospitalized. She received her Doctor of Pharmacy degree from Massachusetts College of Pharmacy and Health Sciences. After graduation, Emilie completed a postgraduate pharmacy residency at Bon Secours Memorial Regional Medical Center in Virginia. Her background includes caring for critical care, internal medicine, and surgical patients.

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