Hashimoto’s thyroiditis is the most common cause of hypothyroidism in the United States. Yet, many women are diagnosed with “hypothyroidism” and prescribed medication without ever being told they may have an underlying autoimmune condition. From a functional medicine perspective, this is a crucial oversight.
In this article, we’ll explore how Hashimoto’s thyroiditis is often mismanaged under conventional models of care, how functional medicine offers a root-cause, immune-focused approach, and why healing requires more than just thyroid medication.
How Common Is Hashimoto’s in Hypothyroid Women?
Up to 90% of women diagnosed with hypothyroidism in the U.S. actually have Hashimoto’s thyroiditis—an autoimmune condition in which the immune system attacks the thyroid gland. Unfortunately, most of these women are never tested for thyroid antibodies, leaving the true cause unaddressed.
This is one of the key distinctions between functional medicine and conventional care. In functional medicine, we recognize that Hashimoto’s is not primarily a thyroid disorder. It is an immune system imbalance that results in damage to the thyroid. To truly support these patients, we must treat the immune system first, not just medicate the thyroid.
What Is Hashimoto’s Thyroiditis?
Hashimoto’s thyroiditis is an autoimmune disease that leads to chronic inflammation of the thyroid gland. Over time, the immune attack reduces the gland’s ability to produce adequate thyroid hormones, which control metabolism, energy production, brain function, and more.
Common symptoms of Hashimoto’s include:
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Chronic fatigue
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Weight gain
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Hair thinning or hair loss
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Brain fog and memory problems
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Depression and mood swings
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Irregular menstrual cycles
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Dry skin and cold intolerance
Hashimoto’s progresses slowly and often goes undiagnosed for years. Even when it’s finally detected, the conventional solution of prescribing levothyroxine doesn’t resolve the underlying immune activity.
Conventional Treatment vs. Functional Medicine Approach
Conventional Approach:
Western medicine focuses on managing thyroid hormone levels, typically by prescribing levothyroxine (T4). While this helps normalize lab values, it often fails to resolve the root cause of Hashimoto’s—autoimmune dysfunction.
Functional Medicine Approach:
Functional medicine treats the whole person, not just the lab values. Rather than masking symptoms with medication, we investigate why the immune system is attacking the thyroid, and we develop a plan to calm the immune system and heal the body from the inside out.
This means:
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Identifying food sensitivities and environmental triggers
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Supporting gut health
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Managing chronic stress and cortisol imbalances
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Addressing nutrient deficiencies
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Treating stealth infections
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Improving detoxification pathways
In short, we support the thyroid by supporting the whole system.
Thyroid Medication Isn’t the Whole Story
Many patients are shocked to discover that despite taking thyroid medication, they still feel tired, foggy, bloated, or depressed. Why? Because thyroid hormone replacement doesn’t stop the autoimmune attack or address the multifactorial drivers of dysfunction.
Some of the most common root causes of Hashimoto’s include:
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Leaky gut and dysbiosis
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Chronic infections (e.g., Epstein-Barr virus, H. pylori)
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Gluten and dairy sensitivities
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Heavy metal and environmental toxicity
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Blood sugar imbalances
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Chronic stress and adrenal dysregulation
Addressing these issues is critical for sustainable symptom relief and disease management.
You Must Support the Immune System—Not Just the Thyroid
Hashimoto’s is an immune system problem that affects the thyroid. If you’re only treating the thyroid, you’re missing the bigger picture.
A functional medicine approach focuses on:
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Elimination diets (to uncover inflammatory foods)
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Gut healing protocols (including glutamine, zinc, and probiotics)
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Anti-inflammatory nutrition (rich in omega-3s, antioxidants, fiber)
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Detoxification support (through nutrients and lifestyle practices)
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Adrenal restoration (adaptogens, stress reduction, balanced sleep)
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Targeted supplementation (like selenium, vitamin D, iron, and magnesium)
Healing Hashimoto’s requires working with the immune system, not against it.
Functional Medicine Testing for Hashimoto’s Thyroiditis
Another major advantage of functional medicine is comprehensive lab testing. Conventional doctors often only test TSH (thyroid-stimulating hormone), which provides an incomplete picture. In functional medicine, we order a full thyroid panel, which includes:
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TSH
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Free T4
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Free T3
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Reverse T3
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Total T4
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Total T3
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TPO antibodies (thyroid peroxidase)
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Thyroglobulin antibodies (TgAb)
We also evaluate related systems and markers, including:
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Cortisol levels (saliva or DUTCH test)
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Fasting glucose, insulin, and HbA1c
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Comprehensive stool and GI testing (GI-MAP or similar)
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Micronutrient analysis
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Food sensitivity testing
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Heavy metal and environmental toxin exposure
This level of testing allows for a highly personalized protocol based on the root drivers unique to each patient.
Healing Is Possible: What You Can Expect
With a targeted, holistic approach, many Hashimoto’s patients experience:
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Improved energy and mood
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Better digestion and metabolism
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Weight loss or stabilization
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Clearer skin and reduced hair loss
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Decreased brain fog and improved memory
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Reduced autoimmune antibody levels
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Greater overall vitality
It’s important to understand that autoimmune conditions can go into remission, especially when triggers are removed and healing systems are supported.
Consistency is key. Healing takes time, but it is possible.
You Deserve Answers—And Real Solutions
If you’ve been told you have hypothyroidism but still feel unwell, it may be time to dig deeper. Whether you’ve been diagnosed with Hashimoto’s thyroiditis or suspect something is being missed, a functional medicine approach offers a comprehensive path to understanding your symptoms—and finding real relief.
Hashimoto’s doesn’t have to define your life. You can regain your energy, focus, and health with the right guidance.
Next Steps
We help patients uncover the root causes of thyroid dysfunction every day. If you’re ready for real answers, not just prescriptions, contact our clinic today at (949)476-1250 to schedule a consultation. Let’s find out what’s driving your symptoms and build a healing plan tailored to you.