It’s Not Your Thyroid’s Fault — Here’s What’s Really Going On

by Dr. Krista Morton

If you’re part of the approximately 5% of the U.S. population diagnosed with an autoimmune thyroid condition, you’ve likely heard the phrase, “your body is attacking your thyroid gland.” We will dismantle this inaccurate—and unfortunately common—phrase in the content below and help you understand what may be the real catalyst for the expression of autoimmune thyroid conditions, as well as the role that toxic mold and mycotoxins play. In my clinical experience, almost all of my patients who present with thyroid disease, especially autoimmune thyroid disease, have an underlying issue of mycotoxins in the body contributing to their thyroid health.

The human body, in all of its innate intelligence and divine design, works as a whole system—not as isolated organs. Think back to the “Dry Bones” song you may have learned in anatomy class: “the ankle bone’s connected to the shin bone,” etc. This is actually a great framework for understanding where we may look for local root causes of systemic issues. In the case of the thyroid gland, what tissues, glands, and cavities are local to the thyroid, and what systems have a relationship in controlling thyroid function? This is the launchpad for understanding individual root causes of autoimmune thyroid conditions, and this framework can be applied to other autoimmune diseases as well.

When we look at where the thyroid is located in the human body, we find that it sits in the throat area, surrounded upstream by glands and cavities that drain down the throat: the sinuses, teeth, tonsils, and upper lymphatic/glymphatic chain vessels. In its physiological setup, the thyroid is the canary in the coal mine for toxicity in these local tissues. Now consider the organs and systems that influence thyroid function: the liver, small intestine, the HPA axis (hypothalamic‑pituitary‑adrenal axis), and the cell membranes. The pituitary gland orchestrates the beginning of thyroid hormone production. It produces TSH (thyroid‑stimulating hormone), which signals the thyroid gland to produce T4 (the inactive thyroid hormone), which is then converted to T3 (the usable, active thyroid hormone that contributes to your body’s metabolic fire). T4 is converted to T3 primarily in the liver and small intestine, while a small amount is converted in the thyroid gland itself. Every cell in the human body has a T3 receptor. If the cell membranes are not able to “breathe” properly (cellular respiration) due to low mitochondrial energy and inflammation of the inner and outer membranes, the cell often becomes resistant to “hearing” your hormones, including T3.

How Mycotoxins Enter the Picture

When we zoom out and look at the local tissues and the relational tissues connected to the thyroid gland, it becomes clear that the thyroid gland itself is highly unlikely to be the culprit of dysfunction and autoimmunity. Instead, we must ask: what toxicity is driving dysfunction in these other glands, tissues, and metabolic processes? This is where mycotoxins enter the picture.

Let’s begin with the local tissues. Toxic mold is inhaled through the nose, producing excess mucus due to histamine release and potentially colonizing the nasal cavities. This drainage travels down the back of the throat (often called “morning phlegm” or allergies), frequently accompanied by puffiness in the upper lymphatic chain, morning drainage headaches, and brain fog. Now, the thyroid gland lives in a “toxic neighborhood.” With mycotoxins dripping down the back of the throat and invading the tissues of the thyroid gland, the body attempts to defend the thyroid by eradicating the mycotoxins—but the thyroid tissue gets caught in the crossfire. This is where the misconception arises that the “body is attacking itself.” It’s not attacking itself; it is attacking foreign toxins or pathogens that should not be in or around the tissue.

To understand the upstream effects of fungal nasal colonies on the thyroid gland, we look to the pituitary gland. Fungal colonies constantly off‑gas mycotoxins (microscopic mold spores), which vaporize upward and, over time, erode the thin barrier between the nasal passages and the pituitary gland. This creates dysfunction in the HPA axis, often leading to issues with the pituitary’s responsibility of signaling the thyroid gland via TSH production, in addition to dysregulating the multitude of other tasks the pituitary performs.

Liver congestion is common, as bile flow becomes inhibited by toxicity, and mycotoxins slow down the body’s detoxification pathways. Mycotoxins heavily burden the liver and often colonize the gut—two primary areas where T4 converts into T3. Mycotoxins also suppress mitochondrial function and inflame cell membranes, preventing cells from “hearing” the thyroid hormones circulating in the blood. This is why so many patients walk around with undiagnosed thyroid disease: the hormones circulate in the blood, making labs appear “normal,” while the cells cannot use the hormones, leaving the patient with “normal labs,” unusable thyroid hormone, and mystery symptoms.

Often, in lab work, TSH is the last marker to go out of range, typically in stage 3 or 4 of thyroid disease. This highlights the importance of a full thyroid panel: TSH, Free T4, Free T3, Total T4, Total T3, Reverse T3, TPO antibodies, and TGAb antibodies. Frequently, the first marker to be out of range in thyroid disease will be T3 or thyroid antibodies.

There are numerous ways the thyroid gland can become dysregulated via relational organs and systems. This should not be dismissed in root‑cause thyroid care—we don’t want to focus solely on the thyroid itself, but also the surrounding tissues and the relational systems. This brings us to support strategies. The following are some of my favorite ways to support patients with thyroid disease. As someone who has had a raging case of Hashimoto’s Thyroiditis myself due to mold toxicity and other infections—and is now in autoimmunity remission—I can attest to these tools. Always consult a provider who can help identify your root cause.

Local Support

Thyroid nutrients: Supporting the thyroid gland while addressing the root cause is instrumental in healing. Leveraging proper nutrients—according to your body’s individual needs—such as a thyroid glandular, selenium, iodine, and B vitamins can be essential in laying a foundation for healing.
Nasal rinsing: I have almost all of my autoimmune thyroid patients nasal rinsing. This is vital for clearing out the consistent off‑gassing of mycotoxins in the sinuses. I often recommend Micro Balance Health Products’ Nasal Rinse Bundle and have patients rotate between a CitriDrops rinse and a saline rinse with a pinch of Micro Balance Health Products’ Chitosan Bioflav (a great binder and biofilm buster for fungal and bacterial colonies in the sinuses—be advised for allergies, as this product is derived from shellfish).
Check home, work, and car air quality for mold, and optimize with air purification systems. I advise patients to start with Micro Balance Health Products’ EC3 Mold Screening Test Kit as a starting point for evaluating air quality.
Laser therapy: Laser therapy has shown incredible clinical outcomes for reversing autoimmunity and restoring thyroid function. In a study evaluating low‑level laser therapy for autoimmune thyroiditis, 47% of patients reversed their autoimmunity and discontinued thyroid medications after only 10 treatment sessions (Hossein‑Khannazer et al., 2022). The most effective at‑home laser is the True Laser Pro. Use code KRISTA10 to save 10% at https://go.truelaserpros.com/?am_id=kristamortonkill8748
Check for cavitations and candida in the mouth: The health of your oral microbiome and teeth—similar to sinus drainage—can contribute to toxicity around the thyroid gland. See a biological dentist, get a cone beam scan, and elevate your oral hygiene with oil pulling, tongue scraping, and remineralizing powders.
Lymphatic support: This can be as simple as hitting your “big six” lymph points (a quick search will show you the technique), using a gua sha focused on the upper lymphatics, infrared sauna, or seeing an LMT who specializes in lymphatic drainage. One of my favorite lymph support tricks for thyroid conditions is having patients place their hands (in addition to their feet) on a vibration plate. It gets things moving.

Systemic / Relational Organ and Pathway Support

Liver support: Using liver‑supportive herbs such as milk thistle, schisandra, digestive bitters, or NAC can help the liver regain the support it needs to efficiently convert T4 to T3 again.
Gut support: Saccharomyces boulardii is a helpful probiotic that also acts as a mycotoxin gut binder, helping pull toxicity from the gut and restore microbial balance. Smilax (sarsaparilla root) is another gentle and effective mycotoxin gut binder. These tools help restore small‑intestine function and support T4‑to‑T3 conversion.
Mitochondrial support: Get your membranes moving again. This can be accomplished with PC (phosphatidylcholine), omega‑3s, CoQ10, and methylation B vitamins. This allows your cells to “hear” your thyroid hormones again.
HPA axis support: CellTropin by Micro Balance Health Products is one of my favorite go‑to’s for HPA axis support. It is formulated to restore HPA axis function and support the nervous system after mold exposure.
Avoid gluten: Gliadin, an enzyme in gluten, provokes an autoimmune attack in autoimmune thyroid patients via molecular mimicry. The body confuses gliadin with thyroid cells and provokes an autoimmune response.
Trapped emotions: Address any trapped emotions related to communication, not being “heard,” or something “too difficult to swallow.” These somato‑emotional factors can contribute to thyroid dysfunction. A case report on hypothyroidism and Neuro‑Emotional Technique (NET) showed that 20 sessions over 12 weeks helped reverse thyroid disease (Bablis et al., 2024). Don’t underestimate the mind‑body connection.

Laying the foundation for the systemic processes and contributing factors to optimal thyroid function opens up a more thorough understanding of the relationship between mycotoxins and thyroid function, along with better tools to address the root cause. The thyroid gland is the messenger that there is toxicity somewhere. Until we locate the root cause, eradicate toxins, and restore function to all contributing tissues, we will remain stuck believing that the “body is attacking itself,” and you’ll remain stuck on thyroid medication forever. I don’t know about you, but I wanted more for myself—and I continue to want more for my patients—celebrating each detection of the root cause and each reversal of autoimmune thyroid disease. Your body was designed to heal. Remember: if there is unexplained autoimmunity, there is missing information.

Next time you hear the misconception that your body is “attacking itself,” remember these truths: your body is not the problem, your symptoms are messengers, and their expression is almost always an attempt to protect you from an underlying toxin or infection.

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