The Root Causes of Autoimmune Disease: What Your Doctor Isn't Testing For
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If you've been diagnosed with an autoimmune disease — Hashimoto's thyroiditis, lupus, rheumatoid arthritis, multiple sclerosis, or any other condition on the growing list — you've probably been told the same thing: your immune system is attacking itself, here's a medication to suppress it, and we'll monitor you from here.
What you likely weren't told is why your immune system started attacking in the first place.
That question — the root cause question — is exactly where conventional medicine falls short and where functional and integrative medicine begins. Because autoimmunity doesn't happen in a vacuum. It is a downstream signal of a body under siege, and until you address what's driving the immune dysregulation, you're managing symptoms, not solving the problem.
In this article, I'm walking you through the most common functional root causes of autoimmune disease, including the ones that are routinely overlooked: food sensitivities, gut dysfunction, chronic stress, systemic inflammation, and environmental illness including mold toxicity. If you've been searching for answers around what causes autoimmune flares, natural approaches to autoimmune disease, or why your autoimmune condition isn't improving, keep reading.
What Is Autoimmune Disease — And Why Is It Increasing?
An autoimmune disease is a condition in which the immune system loses its ability to distinguish between foreign invaders and the body's own tissue — and begins attacking itself. Depending on which tissue is targeted, the condition gets a different name. Hashimoto's attacks the thyroid. Rheumatoid arthritis attacks the joints. Lupus can attack virtually any organ system.
What's alarming is that autoimmune disease is one of the fastest-growing categories of chronic illness in the United States. The National Institutes of Health estimates that autoimmune diseases affect roughly 24 million Americans — and many researchers believe the number is significantly underreported, because subclinical autoimmunity (such as a positive ANA test without a formal diagnosis) is extremely common and often dismissed.
The conventional medical approach treats autoimmunity as a malfunction to be suppressed — typically with corticosteroids like prednisone for acute flares, or long-term biologic medications that broadly dampen immune activity. These can absolutely have a role in acute management, but they do nothing to address the underlying triggers. And unaddressed triggers mean ongoing immune dysregulation, ongoing inflammation, and a body that stays in a perpetual state of attack.
The Functional Root Causes of Autoimmune Disease
From an integrative medicine perspective, autoimmunity is not a mystery. It is a predictable outcome of a body that has been burdened beyond its capacity to compensate. Here are the root causes I investigate with every client dealing with a chronic autoimmune condition:
1. Gut Dysfunction and Leaky Gut Syndrome
The gut is the foundation of immune function — approximately 70–80% of your immune system lives in your gastrointestinal tract. When the gut lining becomes compromised (a condition commonly referred to as intestinal permeability or "leaky gut"), it creates a cascade of immune reactivity that can set the stage for autoimmunity.
A leaky gut allows partially digested food particles, bacterial endotoxins, and other antigens to pass into the bloodstream. Your immune system — encountering these particles in a place they should never be — mounts an immune response. Over time, through a process called molecular mimicry, the immune system can begin to confuse the proteins from these foreign particles with proteins in your own tissue. This is one of the most well-documented mechanisms by which autoimmunity develops.
Restoring gut integrity — through targeted nutrition, removing inflammatory foods, supporting the gut lining, and addressing dysbiosis — is foundational to any serious autoimmune recovery protocol.
2. Food Sensitivities as a Trigger for Autoimmune Disease
This is one of the most underappreciated and undertested drivers of autoimmune conditions, and it's something I work on with almost every single client I see.
Food sensitivities are not the same as food allergies. They're not anaphylactic, they don't show up on a standard allergy panel, and they often develop gradually — which is exactly why they're so easy to miss. But their impact on the immune system can be profound.
Here's what's happening mechanistically: when you have a leaky gut, food proteins that are only partially broken down pass into the bloodstream. Your immune system tags them as threats and builds antibodies against them. Over time, if those food proteins share a structural resemblance with proteins in your own tissue — again, molecular mimicry — your immune system starts attacking both. You eat the food, you trigger an immune response, and that immune response contributes to your autoimmune flare.
The most common culprit I see clinically is wheat and gluten. The gluten protein, gliadin, has been extensively studied for its ability to trigger immune reactions that cross-react with thyroid tissue (highly relevant for Hashimoto's), nervous system tissue, and joint tissue. This is why so many people report dramatic improvement in their autoimmune symptoms when they adopt a carnivore, Paleo, or autoimmune protocol diet — they've accidentally removed gluten.
However — and this is important — many of these diets also become very low-carbohydrate in practice, which creates a different set of problems, particularly for women. Chronic low-carb eating depletes hepatic glycogen, stresses the adrenal axis, and can disrupt the hormonal and metabolic environment over time. This is not a sustainable or ideal long-term solution.
My clinical recommendation for most clients with autoimmunity is a normal-carbohydrate Paleo-style framework — one that eliminates wheat and dairy, prioritizes anti-inflammatory whole foods, and is aggressive with fruits, root vegetables, and other whole food carbohydrates to maintain healthy macronutrient ratios and metabolic function.
The problem with gluten is most people think "Oh, I don't have celiac and tested negative for a gluten allergy". This is not the same as in functional health where gluten sensitivity (different than allergy) can trigger systemic inflammation contributing to autoimmune. When I have someone I am working with dealing with ongoing inflammation and autoimmune, the first thing we do is remove things like gluten from their diet.
Beyond gluten, other food sensitivities vary person to person. Dairy, eggs, soy, corn, and nightshades are common offenders. I've seen clients whose autoimmune symptoms dramatically improved simply from identifying and removing a single food sensitivity that had never been on their radar. Testing — specifically through a comprehensive food sensitivity panel — takes the guesswork out of this process entirely
3. Chronic Stress and Ongoing Systemic Inflammation. Chronic stress is not just a mental health issue. It is a full-body physiological state with direct, documented consequences for immune function — and it is one of the most significant and most overlooked drivers of autoimmune flares.
Here's the bioenergetic reality: when your body is under chronic stress — whether that's psychological stress, physiological stress from illness, poor sleep, blood sugar dysregulation, or any other ongoing demand — your adrenal system maintains elevated cortisol output. In the short term, cortisol is anti-inflammatory and immunosuppressive, which is actually protective. But over time, chronic cortisol elevation leads to cortisol resistance, where the immune system stops responding appropriately to cortisol's anti-inflammatory signals.
The result is unchecked, chronic, low-grade inflammation. And chronic inflammation is not a passive state — it is an active energetic burden on the body. Energy that should be going toward tissue repair, hormone production, detoxification, and cellular regeneration gets hijacked to manage the ongoing inflammatory fire.
I see this a lot in my active, fitness enthusiasts crowd who are working out 4-5x/week because while exercise is great for overall health, it is still a stress on the system. On top of that, I find most active individuals are not allowing enough recovering time between sessions that ends up putting the body in a constant low grade state of inflammation.
Add to this if someone is underfueled in comparison to the energy being expended in their workouts (this is something I am seeing a lot of in the low carb, keto, fasting world), and you are not only putting a stress on the nervous system, but also on the immune system which can then trigger autoimmune flare ups.
I talk more about the importance of the right nutrition in detail here in this video conversation.
For someone with an autoimmune condition, this creates a vicious cycle:
- Autoimmunity drives inflammation
- Inflammation creates physiological stress
- Physiological stress disrupts immune regulation
- Disrupted immune regulation worsens autoimmunity
You cannot address autoimmunity without addressing the inflammatory and stress load on the body. This means looking not just at what you're eating, but at sleep quality, nervous system regulation, blood sugar stability, micronutrient sufficiency, and the overall metabolic burden the body is carrying. Tools like limbic system retraining and vagal nerve support — which I incorporate into my clinical programs — are not "extras." For many people dealing with chronic autoimmunity, they are essential.
4. Oxidative Stress and Mitochondrial Dysfunction
Autoimmunity and oxidative stress have a bidirectional relationship — each makes the other worse. Free radical accumulation damages the tissues being targeted by the immune system, and that tissue damage amplifies the immune response. Meanwhile, the chronic inflammatory state of autoimmunity generates additional free radicals, further burdening the system.
Supporting antioxidant status and mitochondrial function is a core part of managing autoimmune conditions from a functional perspective. Nutrients like glutathione, vitamin C, alpha-lipoic acid, CoQ10, and curcumin all have documented roles in reducing oxidative burden and modulating immune activity. Curcumin in particular has been studied across multiple autoimmune conditions for its ability to reduce NF-kB driven inflammation — one of the key inflammatory pathways involved in autoimmune pathology.
5. Environmental Illness — Mold Toxicity and Toxic Burden
This is the piece that most practitioners miss entirely — and for a significant subset of people with chronic, treatment-resistant autoimmune conditions, it may be the most important.
Environmental illness — and specifically mold toxicity (also called chronic inflammatory response syndrome, or CIRS) — is one of the most potent triggers of immune dysregulation I work with clinically. Mycotoxins, the toxic byproducts produced by certain mold species, are immunotoxic. They directly disrupt immune regulation, drive chronic inflammation, impair detoxification pathways, and can trigger or significantly worsen existing autoimmune conditions.
What makes mold toxicity particularly insidious is that it is frequently undetected. Standard medical panels don't test for it. Symptoms overlap with dozens of other conditions — fatigue, brain fog, joint pain, hormone disruption, recurrent illness, heightened chemical sensitivities. Many people with mold-related illness have seen multiple specialists and received diagnoses like fibromyalgia, chronic fatigue, Hashimoto's, or undifferentiated autoimmune disease — without anyone looking upstream at the environmental exposure driving it all.
I speak from both clinical experience and personal experience here. My own health journey involved mold toxicity, and it fundamentally shaped how I approach chronic illness. When you are living or working in a water-damaged building or have a history of mold exposure, that toxic burden must be assessed and addressed — because no amount of dietary intervention, supplementation, or immune modulation will fully resolve autoimmunity in the presence of an ongoing mycotoxin load.
You can hear and learn more about my story in this video.
Testing is the starting point. The MycoTOX urine test is the gold standard for identifying mycotoxin exposure and gives us a concrete picture of your specific toxic burden so we can build a targeted detox protocol around it.
6. Chronic Stealth Infections
A pattern frequently observed in functional medicine is that autoimmune conditions are sometimes preceded by a significant illness — a flu that never fully resolved, a tick bite, a mysterious febrile episode. In some cases, infections with Lyme disease, Epstein-Barr virus, or other tick-borne or stealth pathogens may be driving or amplifying autoimmune activity through mechanisms of molecular mimicry or general immune hyperactivation. Testing for these chronic infections can reveal a missing piece in a complex autoimmune picture.
What to Do Next — Getting to Your Root Cause
If you've been living with an autoimmune condition and feel like you've been managing symptoms rather than actually healing, you're not wrong. The conventional model wasn't designed to ask the root cause questions — but those questions are exactly where the answers live.
Here's what I want you to know: your immune system didn't turn against you randomly. There are identifiable, testable, addressable reasons why your body is in this state. And when you address those reasons systematically — gut health, food sensitivities, inflammatory load, stress physiology, toxic burden — the body has a remarkable capacity to recalibrate.
You have two ways to work with me:
→ Book a 1:1 Telehealth Consultation If you're ready for a personalized deep-dive into your autoimmune condition, I'd love to work with you directly. In our session, we'll look at your full health history, identify your likely root cause drivers, and build a clear, actionable protocol specific to your body and your case.
→ Order Your At-Home MycoTOX Test Kit If you suspect mold or mycotoxin exposure may be contributing to your autoimmune condition — or if you've never been tested and want to rule it out — start with your at-home MycoTOX urine test. It ships to your door, requires no doctor's visit, and gives us real data to work from.
There is a path to true healing and I'd love to help you get you strength, energy and life back.