Thyroid Medication Does Not Always Work: 6 Reasons You Need to Know

Written By


Expert Reviewed By

Dr. Lauryn Lax, OTD, MS

Dr. Lauryn, OTD, MS is a doctor of occupational therapy, clinical nutritionists and functional medicine expert with 25 years of clinical and personal experience in healing from complex chronic health issues and helping others do the same.

Woman Sitting On A Couch Having Thyroid Medication

When it comes to thyroid medication, there is no one-size-fits-all answer.

Medication is often viewed as the “panacea” in conventional healthcare.

Headache? Pop an Advil.

High blood pressure? Take a statin.

Unwanted weight gain, fatigue or swelling?

Thyroid medication to the rescue.

Woman Sitting On Her Bed Holding A Cup Having Thyroid Medication

Thyroid medication, specifically levothyroxine (Levothyroid® Synthroid®, Levoxyl®, and Armour®),  are the most prescribed drugs in the nation—ranking above statins, SSRI’s and the birth control pill. Since many conventional practitioners do not typically consider the different variations of thyroid disease (i.e. Overt vs. Subclinical vs. Secondary vs. Autoimmune), any sign of an “off” thyroid marker must mean you need a replacement.

In theory, this sounds good—especially if you are feeling the effects of a thyroid condition. If you have a thyroid issue, you can’t wait to start taking your thyroid medication to make the dreadful symptoms go away – good bye constant fatigue, brain fog, stubborn weight gain, headaches, sleepless nights, depressed moods, and so on.

However, what happens if you take your medication and still don’t feel any better? Even when blood tests (TSH & TH) suggest that thyroid function is “back to normal,” many individuals still feel like they did prior to the medication.

Unfortunately, thyroid formulas are not always the panacea they are made out to be, often yielding mixed or subpar results for some—especially if you’re not on the right formula for you.

Here are 6 reasons your thyroid medications may not work:

1. You’re Not Absorbing the Thyroxine Hormone in the Medicine

Simply put, if you have a gut or liver issue, your body will not metabolize the thyroid medication properly.

2. You’re Overdiagnosed or Overtreating a Thyroid Problem

Your thyroid may not be the issue. Common culprits behind “thyroid symptoms” include:

  • Underlying gut pathologies (bacterial overgrowth, low stomach acid, parasitic infection, bacterial infection, H. pylori)
  • Chronic stress & HPA Axis Dysfunction (adrenal, cortisol and hormone imbalances)
  • Underfunctioning pituitary (controls the growth, development and function of other endocrine glands)
  • Environmental toxic burden
  • Low immune function
  • Reduced oxygen to cells (iron deficiency or in some cases, iron overload)
  • Blood sugar imbalances
  • Other chronic diseases, inflammation or underlying infections (Lyme disease, hepatitis C, IBD, etc.)
  • Long-term medication use or drug-induced hypothyroidism (overdose of thyroid hormones or other hormones)
  • Nutrient deficiencies (selenium, copper, iodine, zinc, pyridoxal 5 phosphate, zinc, magnesium)

3. You Have a T4—>T3 Conversion Problem (Not a Thyroid Problem)

Your cells must be able to convert T4 to T3, the active form of thyroid hormone, in order to produce energy. If they can’t make the conversion, you may still experience thyroid symptoms while on the medication. What causes poor conversion? Inflammation! Inflammation decreases the conversion of T4 to T3. T4 is the inactive form of thyroid hormone. Furthermore, the body has to convert it to the active T3 form before it can be used. Most synthetic hormone medications on the market are T4. If you give a T4 medication (like Synthroid, Levoxyl, Unithroid, etc.) to a person with inflammation already, it’s not going to work because they can’t convert the T4 to T3.

On bloodwork, a red flag that you’re having conversion issues is having low levels of T3 with normal T4 and either low or normal TSH—also known as “low T3 syndrome”. Although it does involve low levels of T3 (the most active form of thyroid hormone), it is not caused by a problem with the thyroid gland.

Low T3 Syndrome is a byproduct of the following “inflammatory” issues:

  • Chronic stress (HPA Axis Dysregulaton) and increase in inflammatory markers (particularly inflammatory cytokine TNF-alpha)
  • Under-active pituitary function (your pituitary cannot produce thyrotropin to then produce T4 and T3)
  • Gut or liver issues (20% of your active thyroid hormone (T3) is converted in your gut and the remaining 80% is converted by other organs, especially the liver, brain, skeletal muscle and kidneys)
  • Alterations in the carrier proteins that transport T4 and T3 hormones throughout your body (due to stress or nutrient deficiencies)
  • Changes in YOUR thyroid hormone receptors (THR)—inhibiting or over consuming thyroid hormones

4. You Have Autoimmune Thyroid

Woman Glass On The Table Worried About Her Thyroid Medication

Hashimoto’s and Grave’s disease are inflammatory conditions wherein the thyroid attacks itself. The top twos driver of autoimmunity are intestinal permeability (“leaky gut”) and triggers (inflammation) that “turn on” the genes of autoimmunity—not poor thyroid function.

If you’re taking a thyroid medication for a condition—particularly if you have an undiagnosed autoimmune condition—but you’re not addressing your gut health, inflammation and personal triggers (from fluoride in your water and toothpaste, to birth control pill use, antibiotic history, mold in your home, etc.) then medicine won’t do a body good.

5. You’re Medications are Contraindicated

Interestingly, many medications—or supplements for that matter—produce drug interactions with thyroid  medication. For instance, estrogen found in birth control pills can exacerbate thyroid dysfunction. Even slight alterations in the dosing or absorption of medications can impact the effect of thyroid hormones. Additionally, do your research on what you are currently taking to uncover for yourself how medications may affect the assimilation or absorption of thyroid hormones.

Beyond interactions as well, medications for other health conditions may have a direct effect on the health of your thyroid in other ways—destroying thyroid cells and tissue, impacting natural thyroid hormone production and triggering the immune processes of the thyroid gland.

According to pharmacist Isabella Wentz, the top 9 drugs and chemicals that may affect thyroid function include:

  • Lithium (SSRI for bipolar, depression)
  • Amiodarone (heart disease)
  • Fluoride (toothpaste, water)
  • Hormone Replacement or Birth Control
  • Proton Pump Inhibitors (PPI’s for acide reflux)
  • Interferon (cancer drug)
  • Accutane (skin conditions)
  • Iodine (contraindicated if you have a selenium deficiency or you do not have a true iodine deficiency)
  • Botox (plastic surgery)

Also, if medical reasons warrant your thyroid medication use, it is even more important to optimize essential nutrients including probiotics and prebiotics, magnesium, zinc, B-vitamins and glutathione.

6. You’re Taking the Wrong Dose or Type of Medicine for You

The strength and power of your thyroid changes over time—it fluctuates with the change of seasons, it gets weaker as you age, and it increases or decreases hormone production as you gain or lose weight or if you are under more stress than usual. However, when we take medication, it works in contrast. We do not modify thyroid medication immediately as we change our weight, as the seasons change or anything else happens to our body. As a result, you can have a mismatch between the medication dose you were prescribed and what your body currently needs.

In addition, unlike supplemental herbs and natural compounds, many medications are “synthetic” (fake)—leaving you feeling less than natural.

A blinded study comparing the effects of natural desiccated thyroid hormone (T4/T3) vs. levothyroxine (synthetic T4) found that the patients who took the more natural version felt better—despite normal blood work results on both trials. In the study, a total of 70 patients with hypothyroidism were treated with either desiccated thyroid extract or levothyroxine for 12 weeks followed by a switch to other option for another 16 weeks. The participants were “blinded” during both phases—they did not know the type of pill they received. After each treatment period patients were weighed, had blood tests, underwent psychometric testing and were asked which therapy they preferred.

The researchers reported that 49% of the patients preferred desiccated thyroid extract, 19% preferred levothyroxine and 23% had no preference. Desiccated thyroid extract use was also associated with more weight loss. There was no difference in the psychometric testing or in any symptoms. Lastly, both types of thyroid hormone were able to normalize the abnormal thyroid blood tests. Although desiccated thyroid extract is not widely used, this study showed that many patients preferred the more natural option as compared with levothyroxine, potentially worth considering with your healthcare provider if your symptoms are not improving on thyroid medication (1).


  1. Hoang TD et al Desiccated thyroid extract compared with levothyroxine in the treatment of hypothyroidism: A randomized, double-blind, crossover study. J Clin Endo- crinol Metab 2013;98:1982-90. Epub March 28, 2013.


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