Autoimmune Conditions We Treat

A landmark 2024 study published in the Journal of Clinical Investigation — the largest EHR-based prevalence analysis of its kind — found that over 15 million Americans, or 4.6% of the US population, have been diagnosed with at least one autoimmune disease. Women account for 63% of those diagnoses. And 34% of people with one autoimmune condition will develop a second.

These numbers describe a medical category that is growing, underfunded, and persistently undertreated at its roots. Most patients receive a diagnosis and a suppression strategy — medications that quiet the immune attack without investigating what provoked it. Functional medicine asks the question conventional care often skips: why is the immune system attacking you in the first place?

Hashimoto’s thyroiditis is the most common autoimmune disease in the United States and the leading cause of hypothyroidism. It affects an estimated 14 million Americans — with women diagnosed at 8 to 10 times the rate of men, typically between the ages of 30 and 50. Despite its prevalence, many patients go years without a proper diagnosis. Conventional thyroid screening focuses on TSH alone, which can remain in the normal range while thyroid antibodies — the actual markers of autoimmune attack — are actively elevated.

The standard of care after diagnosis is thyroid hormone replacement. This addresses the resulting hormone deficiency but leaves the immune assault completely unaddressed. Patients often report persistent fatigue, brain fog, hair loss, and weight dysregulation even when their TSH is ‘normal’ on medication — because the antibody-driven inflammation has not been investigated or treated.

A functional medicine approach to Hashimoto’s maps the terrain of immune triggers: intestinal permeability, molecular mimicry from infections like Epstein-Barr virus or H. pylori, nutrient deficiencies (particularly selenium, vitamin D, and zinc), dietary antigens such as gluten, and environmental toxin burden. Testing goes beyond TSH to include free T3, free T4, reverse T3, TPO antibodies, and anti-thyroglobulin antibodies. Treatment is layered — supporting hormone levels while actively reducing the autoimmune burden that is driving them down.

Rheumatoid arthritis (RA) affects approximately 1.3 million American adults and is the most common form of autoimmune arthritis in the country. It is not a joint disease — it is an immune disease that expresses through the joints. The distinction matters enormously for treatment. RA involves synovial inflammation driven by immune complexes, and left unmanaged it carries a two-fold increased risk of cardiovascular disease, along with elevated risk of lymphoma and accelerated osteoporosis.

Conventional RA treatment relies on DMARDs (disease-modifying antirheumatic drugs) and biologics to suppress the immune response. These are often necessary — and we support collaborative care with rheumatology. But suppression is not resolution. Research consistently links RA onset and flares to gut dysbiosis, increased intestinal permeability, specific microbial imbalances (including Prevotella copri overgrowth), dietary inflammatory load, and psychosocial stress. These are addressable factors.

Our functional evaluation of RA includes inflammatory markers (hs-CRP, ESR), microbiome analysis, food sensitivity testing, nutrient status (particularly omega-3 index, vitamin D, and magnesium), and toxic burden assessment. The goal is to reduce the inflammatory substrate fueling the immune response — not as a replacement for your rheumatologist, but as a necessary complement to structural treatment.

Psoriasis is frequently described as a skin condition, but the skin is the symptom — not the disease. Psoriasis is a chronic systemic immune condition driven by dysregulated T-cell activity and elevated inflammatory cytokines, particularly TNF-alpha, IL-17, and IL-23. The plaques visible on the skin reflect an immune process that is active throughout the body. Psoriasis is associated with psoriatic arthritis (in up to 30% of patients), cardiovascular disease, metabolic syndrome, inflammatory bowel disease, and depression — all sharing the same inflammatory terrain.

Conventional dermatology manages psoriasis primarily through topical treatments, phototherapy, and systemic biologics. These can be highly effective for skin clearance, but they do not address the underlying immune dysregulation. Flares return because the drivers — leaky gut, food intolerances, stress, alcohol, infections — are still present.

Functional medicine maps those drivers systematically. The gut-skin axis is particularly central: research links psoriasis to specific patterns of gut dysbiosis, increased intestinal permeability, and altered bile acid metabolism. Dietary interventions — particularly anti-inflammatory and gluten-elimination protocols — have demonstrated meaningful reductions in psoriasis severity in peer-reviewed studies. We evaluate the full systemic picture and build a treatment plan that addresses the inflammation from the inside out.

Multiple sclerosis (MS) is an immune-mediated disease in which the immune system attacks myelin — the protective sheath around nerve fibers — leading to communication disruptions between the brain and the rest of the body. MS affects approximately 1 million Americans, with women diagnosed 2 to 3 times more frequently than men. It is one of the most common neurological conditions in young adults.

What is often underemphasized in conventional MS care is the depth of its environmental and lifestyle associations. Vitamin D deficiency is among the most consistently identified risk factors for MS onset and relapse frequency — patients with the lowest vitamin D levels face significantly higher relapse rates. Gut microbiome dysbiosis, Epstein-Barr virus exposure, smoking history, obesity, and low omega-3 fatty acid status have all been associated with MS risk and progression in peer-reviewed research.

Functional medicine does not replace your neurologist’s disease-modifying therapies — these are often essential for slowing structural damage and should be continued as prescribed. Our role is to address the modifiable biological factors running in parallel: optimizing vitamin D and omega-3 status, reducing systemic inflammation, supporting gut microbiome health, addressing nutrient deficiencies, and creating the physiological conditions in which your nervous system has the best opportunity to function and repair.

Despite presenting in different organs and tissues, Hashimoto’s, RA, psoriasis, and MS share a common upstream architecture. Research consistently points to the same cluster of contributing factors: increased intestinal permeability (leaky gut) allowing immune-activating antigens into systemic circulation; chronic low-grade infections triggering molecular mimicry; nutrient deficiencies — particularly vitamin D, selenium, and omega-3 fatty acids — that impair immune regulation; dietary triggers that sustain inflammation; and toxic burden from environmental exposures.

This convergence is why functional medicine’s approach to autoimmunity is not condition-specific — it is systems-level. We investigate the upstream drivers regardless of which tissue the immune system has chosen to attack. The treatment architecture — gut repair, nutrient repletion, infection resolution, dietary modification, toxin reduction, stress physiology support — is largely shared across conditions, calibrated for each person’s unique presentation.

Every autoimmune case begins with a deep timeline review — mapping the sequence of infections, stressors, environmental exposures, dietary changes, and symptom onset. Autoimmune disease rarely appears without a story. Identifying the initiating trigger and the factors sustaining immune dysregulation is the foundation of everything that follows.

From there, we use targeted functional testing to assess the biological systems most relevant to your condition: gut microbiome and permeability, nutrient status, inflammatory load, toxic burden, and relevant autoantibody panels. We interpret results against optimal functional ranges — not just population averages — because the goal is not merely to be within the lab’s reference range. The goal is to feel well.

Treatment protocols are individualized and sequenced. There is an order to addressing autoimmunity effectively: you cannot successfully calm immune reactivity if the gut is still driving antigen load, and nutrient repletion is only sustainable if absorption has been restored. We guide that sequence with you, adjusting as your labs and symptoms evolve.