By Dr. Lisa Ballehr
What’s driving your immune system to attack you? For millions of people living with autoimmune disease, this is the critical question—and one that traditional medicine often fails to fully answer.
Your immune system is designed to defend you. It’s your body’s built-in security system, always on alert to recognize and eliminate harmful invaders like bacteria, viruses, and environmental toxins. But when that system starts to malfunction, it can turn on your own tissues, mistaking them for enemies. That’s when autoimmune disease takes hold.
And while genetics do play a role, they don’t fully explain why autoimmunity is rising at such an alarming rate. The truth is more complex. Environmental and lifestyle factors are often the real culprits driving your immune system to attack you.
Let’s break down what autoimmune disease really is, the common hidden triggers, and most importantly—how you can start healing by addressing what’s pushing your immune system over the edge.
What Is Autoimmune Disease?
Autoimmune diseases occur when the immune system mistakenly targets your own tissues. Instead of fighting off viruses and bacteria, your immune cells begin attacking your joints, thyroid, skin, gut, or nervous system. This creates chronic inflammation, pain, fatigue, and a wide range of symptoms that vary from person to person.
Common autoimmune diseases include:
- Rheumatoid arthritis
- Hashimoto’s thyroiditis
- Lupus
- Psoriasis
- Type 1 diabetes
- Multiple sclerosis
- Celiac disease
While these conditions may seem unrelated, they all stem from one key dysfunction: something is driving your immune system to attack you instead of protecting you.
Why Is This Happening?
Conventional medicine often places the blame on genetics. While there may be a genetic predisposition, that alone doesn’t explain why so many people are now being diagnosed with autoimmune diseases—or why symptoms often begin suddenly in adulthood.
It’s the environmental and internal triggers that tip the balance and ignite the autoimmune process. These are the real factors driving your immune system to attack you, and they often go unaddressed in standard medical care.
1. Chronic Stress: The Invisible Instigator
Chronic stress is more than just a mental health issue—it’s a physiological one. Long-term stress keeps your body in a state of high alert, releasing hormones like cortisol that, over time, suppress and dysregulate immune function.
This heightened stress response can:
- Increase systemic inflammation
- Disrupt immune signaling
- Lead to misfires in immune targeting
Stress doesn’t just aggravate symptoms—it’s one of the root-level forces driving your immune system to attack you. Managing stress with tools like breathwork, meditation, and sleep hygiene is foundational to recovery.
2. Environmental Toxins: The Hidden Burden
From pesticides in our food to chemicals in household cleaners, we’re exposed to more toxins today than ever before. These substances place a heavy load on the liver and detoxification pathways. When your body can’t keep up, toxins accumulate and trigger inflammation.
Your immune system starts seeing normal tissues as dangerous simply because they’re in the line of fire.
Common immune-disrupting toxins include:
- Heavy metals (like mercury or lead)
- Pesticides and herbicides
- BPA and plastics
- Mold toxins (mycotoxins)
These toxic exposures may be silently driving your immune system to attack you without your awareness. Reducing exposure and supporting detoxification is key to restoring immune balance.
3. Infections: The Lingering Threats
Certain infections can act as long-term agitators of the immune system. Even after the acute infection resolves, some microbes remain hidden in the body, keeping the immune system on high alert.
Viruses like Epstein-Barr and bacteria like Borrelia (Lyme disease) are well-documented in their connection to autoimmune diseases. Parasitic and fungal infections can also play a role.
COVID-19 has introduced a new dimension. Many individuals with long COVID report symptoms nearly identical to autoimmune conditions: fatigue, brain fog, joint pain, and persistent inflammation. These aren’t just lingering symptoms—they may be signs that the virus is driving your immune system to attack you.
4. Gut Dysfunction: Autoimmunity’s Silent Partner
About 70% of your immune system lives in your gut. A healthy gut lining acts like a security barrier, keeping harmful substances out of the bloodstream. But when that lining becomes damaged—a condition often called “leaky gut”—undigested food particles, bacteria, and toxins escape into circulation and trigger immune responses.
This constant immune activation can confuse your immune system into targeting your own tissues.
Poor gut health is one of the most overlooked yet powerful forces driving your immune system to attack you.
Signs of gut dysfunction include:
- Bloating, gas, or indigestion
- Food sensitivities
- Skin issues (like eczema)
- Brain fog or fatigue after eating
Healing the gut with an anti-inflammatory diet, probiotics, and gut-repair nutrients can help stop the immune confusion and calm inflammation.
Can Autoimmune Disease Be Reversed?
While mainstream medicine often treats autoimmune disease as a lifelong condition managed with immunosuppressants, Functional Medicine takes a different approach. Instead of silencing the immune system, we aim to understand what’s driving your immune system to attack you—and remove those triggers.
With the right tools and support, it’s possible to:
- Reduce systemic inflammation
- Heal tissue damage
- Restore immune balance
- Reverse or significantly improve symptoms
This doesn’t mean a one-size-fits-all cure, but it does mean hope—and real change—are possible.
The Functional Medicine Approach
Recovery begins with identifying and removing the factors that are disrupting your immune system. This includes:
- Addressing chronic stress through nervous system regulation
- Detoxifying the body by reducing toxic exposure and supporting liver pathways
- Treating hidden infections using targeted diagnostics and therapies
- Repairing the gut with personalized nutrition and gut-supportive supplements
- Restoring balance with anti-inflammatory lifestyle practices
Each person’s autoimmune story is unique, but the path forward always starts with understanding what’s driving your immune system to attack you.
You Don’t Have to Do This Alone
If you’ve been dismissed or told “it’s just stress” while your body continues to struggle, you’re not alone—and it’s not in your head. Autoimmune disease is real, complex, and driven by a combination of factors that can be identified and treated.
As a Functional Medicine physician, I help professionals and high-performers uncover the root causes behind their symptoms and guide them toward sustainable healing.
It’s time to stop fighting your body and start understanding what’s really driving your immune system to attack you.
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