Do Allergies Trigger Autoimmune Disease?

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The Functional Medicine Guide to Understanding Autoimmune Disease + Allergies

To most people, allergy symptoms, Celiac disease, and rheumatoid arthritis might seem like they have many more differences than similarities, but all of these diseases have one thing in common–your immune system.

Allergic diseases and autoimmunity follow a similar developmental path, though their presentation is often quite different. Today, you’ll learn how food allergies impact your risk of autoimmune disease, what exactly causes autoimmune disease in the first place–and more importantly–how you can decrease your risk of autoimmune disease. 

Is it Autoimmune Disease, or an Allergy?Do Allergies Trigger Autoimmune Disease?

When you think about autoimmune disease, you might imagine your immune system mounting an attack on your own tissues—like your pancreas with type 1 diabetes, or the thyroid with Hashimoto’s thyroiditis. 

With autoimmune disease, your immune system mistakenly flags your own cells for destruction.

With allergies, the invaders are otherwise harmless environmental triggers like pollen, peanuts, or pet dander. Your immune system goes on the offensive to rid your body of the invader.

Both of these responses are generated by the immune system, and that’s where their impact on your health begins. So why do they happen? And can integrative medicine help you avoid their triggers?

Immune System Dysfunction

Autoimmune disease occurs when the body’s normal immune response goes haywire, and begins to attack the body’s own tissues, rather than pathogens. Autoimmunity is characterized by four main components (1,2): 

  • An imbalance in T cell function (which produce and suppress the immune response)
  • Self-reactive immune cells that produce autoantibodies
  • An overburdened immune system
  • Systemic inflammation

Two major outcomes of a dysfunctional immune system are allergies and autoimmune disease. 

Autoimmunity Vs. Allergies

The most common form of allergies involves mast cell activation by environmental exposure to an offending antigen, such as food or pollen. However, it’s also been shown that T cells and mast cells can influence one another, shedding more light on the link between allergies and autoimmunity (3). 

Related: The Benefits of Quercetin & Other Natural Antihistamines

Findings reveal that some allergies–like gluten–may play a role in the development of autoimmune diseases, and this is incredibly beneficial to understanding the link between allergies and autoimmunity. More on these allergen triggers in a moment

What Causes Autoimmune Disease?

For an autoimmune disease to occur, you typically need two things:

  • a genetic predisposition
  • a triggering event 

Autoimmune diseases arise from a combination of genetic and environmental factors. Specific variations in genes set the stage for autoimmunity by altering the development or function of immune cells.  

When an Allergy Causes Autoimmune Disease

Recent research highlights certain antigens that play a role in the development of autoimmune disease. While a food allergy or intolerance may seem unrelated to autoimmunity, these findings tell a different story.

The Gluten-Thyroid Connection

The chemical structure of gliadin (the protein in gluten) looks very similar on a molecular level to that of the thyroid gland (4).

When the gliadin protein encounters a leaky gut, it enters the bloodstream undigested, and the immune system flags it for destruction.

Now, the immune system has created antibodies against gliadin in the interest of a swift response the next time it’s detected. 

What does this mean for you? The antibodies to gliadin cause the body to also attack thyroid tissue. Which means if you have autoimmune thyroid disease and you eat a food containing gluten, your immune system will attack your thyroid (5).

Walnut Allergies Leading to Autoimmunity

Walnuts, in addition to inducing allergic reactions in some people, could also promote autoantibody development in an autoimmune skin disease called pemphigus vulgaris (6).

This is one more piece of information that helps identify food allergen triggers for autoimmune disease, and could lead to a dietary elimination therapy for autoimmune diseases. 

Environmental Triggers for Autoimmune Disease and Dysfunction

Gut Dysbiosis or Intestinal Permeability

Healthy gut bacteria help regulate the production and function of certain T cells, as well as different types of microbial enzymes that impact genetic expression (7,8).

A leaky gut, or intestinal permeability, allows normally harmless bacteria to leave the intestine and pass into circulation, triggering inflammation and an immune response.

Environmental toxins

Heavy metals, PCBs, perfluorinated compounds (PFCs or PFOA) are significant risk factors in the development of autoimmune disease. PFCs in particular contribute to the dysregulation of immune function and favoring the development of autoimmune diseases (9). 

Excessive hygiene

In early life, the immune system relies on microbial input to develop normally. That is, exposure to bacteria and microbes from germs, dirt, and other environmental materials. 

GlutenDo Allergies Trigger Autoimmune Disease?

As mentioned above, gluten is problematic for those at risk of autoimmune thyroid disorders. In addition, gluten has been shown to increase intestinal permeability through its impact on tight-junctions (10). 


Chronic infections, Candida, H. pylori, or others can trigger immune dysregulation as the body tries to clear the infection. 


On some estimates, as much as 50% of autoimmune onset can be attributed to a stressful environmental trigger (11). This stress can be emotional, physical, or internal. Many people report high emotional stress in the period leading up to an autoimmune presentation. 


Women are at increased risk of developing autoimmune conditions, especially within the first year after birth (12). 

Integrative Medicine: Lowering Your Inflammatory and Immune Burden

Autoimmune diseases often flare due to the immune system becoming overstimulated by multiple triggers. By identifying and decreasing common triggers such as food allergies, stress, or environmental toxicities, you can decrease your body’s immune burden giving your immune system more resilience against viruses.

Functional medicine therapies to support immune function include:

  • IV Drip Therapy – A simple and easy way to deliver nutrients directly to cells that need them. You’ll find unique drips at CentreSpringMD to support immunity and boost antioxidant status.
  • MTHFR testing – For individuals with certain genetic variations which affect nearly 40% of the population, extra care is required for a healthy immune response involving methylation processes in the body. Your integrative doctor will help you navigate these factors.

Contact a provider to learn more about individualized autoimmune disease treatment. Remission is possible.

Autoimmune Diet & Lifestyle

Focus on quality proteins, healthy fats, and an abundance of nutrient-dense fruits and vegetables–organically grown, if possible. These will provide you with the micronutrients you need to keep inflammation in check and balance your immune response.

In addition, here are some helpful immune supplements to consider:

  • Vitamin DDo Allergies Trigger Autoimmune Disease?
  • Vitamin C
  • Fermented foods or probiotics
  • Omega-3 fats from fish oil
  • Zinc
  • Inflammation modulating functional foods like turmeric and ginger
  • Immune supportive blends containing astragalus

Lifestyle factors important to lowering your immune burden are:

Get adequate sleep. Chronic insomnia and sleep apnea are both associated with significantly increased risks of autoimmune disease (13).

Stay active. Activities that support healthy blood flow and deep breathing are beneficial. Yoga, stretching, tai chi, and brisk walking are great immune-supportive activities.

Decrease stress. Chronic stress contributes to inflammation and immune dysregulation. Begin intentional relaxation with journaling, therapeutic massage, or meditation.

Integrative Medicine Puts You in Control of Your Immune Health

Autoimmune disease and allergy symptoms share one thing in common–your immune system. And since much of healthy immune function is driven by diet, lifestyle, and overall health, you hold significant power to decrease your risk of autoimmune disease and worsening allergy symptoms.

Your integrative medicine doctor will work with you to identify your genetic risk for autoimmune disease, and develop functional solutions tailored to your individualized needs to maintain or restore balance to your immune health.






Allergies, Autoimmunity, gluten, Immunity

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These statements have not been evaluated by the Food and Drug Administration. These products are not intended to diagnose, treat, cure, or prevent any diseases.
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