What Causes a Food Allergy

What Causes Food Allergies? It All Starts in Your Gut

Food allergies (or more accurately, food sensitivities) are everywhere these days. One person can't handle dairy, another gets brain fog from wheat, someone else's skin breaks out from eggs. Reactions range from mildly annoying to life-threatening anaphylaxis.

Here's what most people don't understand: food allergies aren't caused by the food itself.

Your body isn't supposed to react to salmon or almonds or tomatoes. These are perfectly good foods that humans have eaten for millennia. The real problem is what's happening in your digestive system when these foods arrive.

About 80% of your immune system lives in your gut. When that system starts treating food like an invader, something has gone wrong with the barrier between your intestinal contents and your bloodstream.

That "something" is called leaky gut. And understanding how it works is the key to understanding why you suddenly can't eat foods you've been eating your whole life.

The Gut Barrier: Your Body's Border Security

Your small intestine is about 20 feet long with a surface area roughly the size of a tennis court (when you account for all the villi and microvilli). That's a massive border to protect.

The intestinal lining is only one cell thick. These enterocytes are held together by proteins called tight junctions, which act like adjustable gates between cells. They're supposed to let small, fully-digested nutrients through (amino acids, simple sugars, fatty acids) while keeping large molecules, bacteria, and toxins out.

When these tight junctions work properly, you have selective permeability. Nutrients in, threats out. Simple.

When they don't work, you have intestinal hyperpermeability. Also known as leaky gut.

How the Gut Becomes Leaky: The Zonulin Problem

Here's where it gets interesting. Your gut doesn't just randomly spring leaks.

There's a protein called zonulin that regulates those tight junctions. Think of zonulin as the key that unlocks the gates between your intestinal cells. Your body produces zonulin in response to two main triggers: certain bacteria in your small intestine, and gluten (specifically the gliadin fraction of gluten).

When zonulin levels go up, the tight junctions open wider. This is actually a normal protective response in some situations. The problem comes when zonulin stays elevated chronically, keeping those junctions perpetually loose.

Now large, partially-digested protein molecules can slip through the gaps between cells and enter your bloodstream. Your immune system, which has never seen these large protein fragments before, identifies them as foreign invaders and mounts an attack.

This is when you develop a food allergy.

The Immune Response: Why Allergies Get Worse Over Time

The first time one of these large protein molecules gets through your gut barrier, your immune system produces antibodies called immunoglobulins (Ig). These come in different types (IgA, IgE, IgG, IgM), each designed to fight different kinds of threats.

Your immune system is efficient. Almost too efficient.

The second time you're exposed to that same protein, the response is faster and stronger. Each subsequent exposure generates more antibodies, quicker and more aggressively. This is why food sensitivities usually get worse over time if the underlying gut permeability isn't addressed.

You might tolerate wheat just fine for years, then suddenly start reacting to it. What changed wasn't the wheat. What changed was your gut barrier.

What Actually Causes Leaky Gut

Multiple factors can damage those tight junctions and trigger zonulin release:

Chronic Stress and Cortisol Depletion: This is the big one that almost everyone misses. When you're under chronic stress, your adrenal glands pump out cortisol to help you cope. But cortisol doesn't just manage stress. It also regulates inflammation throughout your body, including in your gut.

When your adrenals become exhausted and can't produce adequate cortisol anymore (what we call adrenal fatigue), you lose that inflammatory control. Your gut lining becomes inflamed, tight junctions loosen, and permeability increases. This is why people with high stress often develop food sensitivities seemingly out of nowhere. (We discuss this connection in depth in our post on what adrenal fatigue actually is and why you might be more stressed than you realize.)

Gut Dysbiosis and SIBO: Your gut contains trillions of bacteria, both beneficial and potentially problematic. When the balance shifts toward pathogenic species (dysbiosis), or when bacteria overgrow in your small intestine where they don't belong (SIBO), the resulting inflammation damages the intestinal lining.

These bacteria can also produce lipopolysaccharides (LPS) and other inflammatory compounds that directly trigger zonulin release. Some bacterial species are particularly good at this, which is why infections or antibiotic use can trigger sudden onset food sensitivities.

Inflammatory Foods: Gluten is the most well-researched trigger for zonulin production. Even in people without celiac disease, gliadin (a component of gluten) binds to receptors in the gut and triggers zonulin release, temporarily increasing permeability. When you eat gluten multiple times daily, that "temporary" becomes chronic.

Other inflammatory foods include processed seed oils, excess sugar, and for many people, dairy proteins. These don't necessarily trigger zonulin directly, but they create inflammation that damages the gut lining over time.

NSAIDs and Medications: Over-the-counter pain medications like ibuprofen, naproxen, and aspirin directly damage the intestinal lining. They inhibit prostaglandin production, which is essential for maintaining the protective mucus layer in your gut. Regular NSAID use is one of the fastest ways to develop leaky gut.

Proton pump inhibitors (PPIs) for acid reflux, antibiotics, and even birth control pills can all contribute by altering stomach acid levels, killing beneficial bacteria, or changing hormone balance in ways that affect gut integrity.

Alcohol: Ethanol is directly toxic to the intestinal lining. Even moderate alcohol consumption increases intestinal permeability. Heavy drinking can cause severe leaky gut within hours.

Low Stomach Acid: Your stomach is supposed to be extremely acidic (pH 1.5-3.5). This acid serves multiple purposes: it activates digestive enzymes, kills pathogenic bacteria and parasites, and begins protein breakdown.

When stomach acid production is inadequate (from chronic stress, aging, PPI use, or H. pylori infection), food doesn't get properly broken down. You end up with larger protein fragments moving into your small intestine, which increases the likelihood they'll slip through a compromised gut barrier.

The Vicious Cycle

Here's where it gets nasty. Leaky gut and food sensitivities create a self-reinforcing cycle:

Stress or inflammation damages your gut lining → Tight junctions loosen → Large food proteins enter your bloodstream → Your immune system attacks them → This immune response creates MORE inflammation → The inflammation damages your gut lining further → More proteins leak through → Stronger immune response → And on and on.

This is why simply avoiding trigger foods often isn't enough. You're treating the symptom (the immune reaction) without addressing the cause (the leaky gut). The gut stays permeable, so you keep developing sensitivities to new foods.

I see this constantly in practice. Someone eliminates wheat, feels better for a few months, then starts reacting to dairy. They eliminate dairy, feel better briefly, then develop sensitivities to eggs or nightshades. The list keeps growing because the underlying permeability problem was never fixed.

The Gut-IBS Connection

This same mechanism explains why so many people with Irritable Bowel Syndrome (IBS) also have food sensitivities. IBS isn't just "stress affecting your stomach." It's often driven by bacterial overgrowth (SIBO), low-grade inflammation, and yes, leaky gut.

When you have intestinal permeability, you're more likely to react to the foods that feed problematic bacteria in your gut. This creates gas, bloating, diarrhea, constipation, all the classic IBS symptoms. The food sensitivities and the IBS are two sides of the same underlying dysfunction.

This is why knowing what foods to avoid with IBS is important, but it's not the whole answer. You need to address the permeability.

Common Symptoms of Food Sensitivities

Food allergy symptoms extend way beyond digestive issues. When large protein molecules and bacterial endotoxins are circulating in your bloodstream, they can affect virtually any system:

Digestive: Gas, bloating, nausea, heartburn, constipation, diarrhea, stomach pain, cramping

Neurological: Brain fog, difficulty concentrating, headaches, migraines, anxiety, depression, mood swings

Skin: Acne, eczema, rosacea, hives, rashes, dry skin, psoriasis

Respiratory: Chronic congestion, post-nasal drip, asthma exacerbation, frequent "colds"

Systemic: Fatigue, joint pain, muscle aches, rapid heart rate, weakness

Oral: Ulcers in mouth or throat, geographic tongue, burning mouth

The diversity of symptoms makes sense when you understand that the immune system is reacting to proteins that shouldn't be in your bloodstream. Those inflammatory signals can affect any tissue.

The Allergy-Immunity Connection

Remember that 80% of your immune system lives in your gut. When your gut is chronically inflamed and permeable, your entire immune system becomes hypervigilant and reactive.

This is why people with food sensitivities often also struggle with seasonal allergies, frequent infections, autoimmune conditions, or chronic inflammation. The gut is the command center for immune function. When it's compromised, everything downstream suffers.

We explore this connection further in posts on seasonal allergy relief and how the hygiene hypothesis affects allergies.

True Allergies vs. Sensitivities

It's worth distinguishing between true IgE-mediated allergies (like nut or shellfish allergies that can cause anaphylaxis) and food sensitivities or intolerances.

True allergies are immediate, severe, and potentially life-threatening. Blood vessels dilate, blood pressure drops, airways constrict. Symptoms appear within minutes: shortness of breath, chest pain, severe abdominal pain, vomiting, diarrhea, weakness, loss of consciousness. If this occurs, it's a medical emergency requiring epinephrine injection and immediate hospital care.

These are the allergies where you carry an EpiPen.

Food sensitivities are usually IgG or IgA mediated, delayed (appearing hours or even days after exposure), and while not immediately dangerous, can make your life miserable with chronic symptoms. These are also far more common and more responsive to gut healing protocols.

Testing and Diagnosis

There are two reliable ways to identify food sensitivities:

Applied Kinesiology Examination: This can identify foods your body is reacting to in real-time by testing muscle response when exposed to suspected allergens. It's particularly useful for identifying hidden sensitivities and assessing digestive enzyme and HCl production.

IgG/IgA Blood Testing: Lab panels can measure antibody levels to dozens or even hundreds of foods. These show what your immune system has been producing antibodies against, which indicates foods you've been reacting to.

Standard allergy testing (skin prick or IgE blood tests) only catches true allergies, not sensitivities, so they miss the majority of food reactions people experience.

The Role of Digestive Function

One of the most common underlying causes of food sensitivities is inadequate digestive enzyme and hydrochloric acid (HCl) production.

If your stomach isn't producing enough acid, proteins don't break down completely. If your pancreas isn't producing enough enzymes, fats and carbohydrates remain partially digested. These larger molecules are more likely to trigger zonulin release and slip through a leaky gut barrier.

Low stomach acid becomes increasingly common with age, chronic stress (there's that adrenal connection again), and long-term use of acid-suppressing medications. Many people taking antacids for "too much acid" actually have too little, and the medications make the problem worse.

Moving Forward: Addressing the Root Cause

Once you understand that food sensitivities are a symptom of gut dysfunction rather than the problem itself, the path forward becomes clearer:

Identify and remove trigger foods (yes, this matters while healing)

Address the underlying causes of leaky gut: chronic stress and adrenal dysfunction, gut infections or dysbiosis, inflammatory foods and medications, low stomach acid and enzyme deficiency

Support gut barrier healing with specific nutrients

Rebalance the microbiome

The good news? Unlike true allergies, food sensitivities are often reversible when you heal the gut. I've seen countless patients successfully reintroduce foods they'd been reacting to for years once the underlying permeability was addressed.

The bad news? It takes time, attention, and addressing multiple systems simultaneously. There's no quick fix. But understanding the mechanism, understanding that your body isn't broken and that bread isn't inherently toxic, that's the first step toward actually healing instead of just managing symptoms.

For comprehensive nutrition strategies that support gut healing and reduce food sensitivities, visit the Fuel Your Body pillar page.

For stress management and adrenal support protocols that reduce gut inflammation, visit the Regulate Your System pillar page.

Ready to optimize your health and performance? Dr. JJ Gregor uses Applied Kinesiology and functional health approaches to help patients identify food sensitivities and heal gut dysfunction at his Frisco, Texas practice. Schedule a consultation to discover how personalized nutrition, gut healing protocols, and stress management can eliminate your food reactions at the root cause.