What’s the Difference Between a Food Allergy and Food Intolerance?

by JJ Virgin on October 18, 2022

Even if you’ve never had one yourself, you’re probably familiar with the aftermath of a food allergy. Think about a peanut allergy, where eating even the tiniest bite can close someone’s throat.  

With a food allergy, the offending food triggers an immediate immune-system response. Your body releases an antibody called immunoglobulin E, or IgE, the most aggressive defense system that your immune system carries.  

IgE antibodies produce quick, dramatic reactions within minutes or even seconds after you eat the problem food. These reactions release large amounts of histamine, which causes swelling, mucus, congestion, and other symptoms.  

At their worst, food allergies create anaphylaxis, a life-threatening reaction that usually occurs within minutes of eating the offending food that impairs breathing, blood pressure, heart rate, and more.   

While they were once rare, food allergies are becoming more common. The most frequently seen food allergies in adults include fish, shellfish, and nut allergies. For children, the most common food allergies include milk, eggs, fish, peanuts (a legume, not a nut), and nuts.1 

“Foods today contain higher amounts of toxic proteins, which can trigger survival mode,” says Alan Christianson, NMD, in The Adrenal Reset Diet. “Because of this, the rates of dangerous allergies to foods like peanuts or shellfish have gone up many-fold during the last few decades. Most experts believe that food allergies are more common today because our foods are higher in chemicals and are different in many ways from how they were in the past.” 

Food intolerance is different. Unlike the immediate response of a food allergy, an intolerance creates a delayed reaction. And unlike food allergies, they aren’t life-threatening. Instead, they trigger another kind of antibody called immunoglobulin G or IgG, which produces symptoms more slowly than IgE antibodies.  

The symptoms of food intolerance can occur several hours or even days after you eat. As a result, you may not make the connection between the offending food and the symptoms it creates.  

Let’s say you ate a piece of bread for dinner on Tuesday and have an excruciating headache Thursday morning. The delayed response, which results when IgG antibodies become activated, keeps your immune system in constant gear and triggers a simmering, low-grade kind of inflammation called chronic inflammation. 

Learn more about chronic inflammation in this blog 

3 Categories of Food Intolerance 

When I say food intolerance, I’m describing negative reactions to certain foods—everything from minor irritation to unpleasant issues that affect your central nervous system, your respiratory system, your digestive system, and your skin.  

Food intolerance can be divided into three categories: 

  1. Food reactions involve eating a food that creates a reaction.  Soy (and foods made from soy, like tofu and tempeh) and gluten, for example, contain goitrogens. These naturally occurring compounds can impair thyroid function by interfering with iodine uptake. 
  2. True Intolerances are when you can’t tolerate a food because you lack a specific chemical or enzyme to digest that food. Lactose intolerance may be the best-known example. Sometimes, true intolerance can be genetic. There’s not much you can do here except avoid that food. 
  3. Food sensitivities create low-grade symptoms over time, such as fatigue, digestive unrest, and joint pain. Some foods are notorious for this bodily response, including eggs, dairy, and gluten. In my experience, I’ve found that about 75% of people experience food sensitivities. 

Since food intolerance can be subtle and usually comes on gradually, connecting the dots between what you eat and how it manifests can be a challenge. 

Weight gain is one clue about food intolerance. How you feel is another huge one. Food intolerance can also have symptoms like headaches, irritability, upset stomach, joint aches, gas and bloating, skin problems such as eczema, and other miserable issues. 

If you’ve been eating a lot of a certain food your system doesn’t like, you eventually exceed your sensitivity threshold, and antibodies build up to fight that food and send your body a message. But by then, you may be struggling with chronic inflammation, weight-loss resistance, and symptoms you may possibly dismiss as normal.  

Why Does Food Intolerance Occur?  

Often, food intolerance develops from leaky gut. Leaky gut and other gut disorders occur because of chronic stress, inflammatory ingredients like gluten and fructose, and prescriptions like antibiotics and other medications.  

Read more about leaky gut here 

“The loss of healthy gut flora, an excess of gut-busting foods, and reliance on medications collectively result in leaky gut, which causes a rise in food sensitivities and food allergies—all of which drive inflammation,” says Mark Hyman, MD, in The Pegan Diet. 

In other words, rarely does one thing create these reactions. Other triggers for food intolerance include:  

  • Genetics (gluten intolerance is especially common). 
  • Inadequate nutrient absorption, which can result in gas, cramping, diarrhea, and even bad breath. 
  • Hormonal interactions with food. I mentioned soy and gluten above as one example. These foods can impair thyroid function. 
  • Dysbiosis, or imbalances in your gut microbiome. Read more about gut imbalances here 
  • Antibiotic medications, especially if you’ve gone through multiple rounds without following up with a probiotic supplement. 
  • Consumption of genetically modified (GMO) foods. 

Compounding that frustration, many foods that cause food intolerance cloak themselves in a faux health halo. You may be eating them and believing you’re doing everything right. 

“People are often shocked when they are told a food they commonly eat and consider to be healthy may be at the root of their problems,” says Vincent Pedre, MD, in Happy Gut. “Unlike IgE-mediated food allergy, the response is not immediate.” 

Because they’re not the usual suspects, these foods may be hard to spot. When I had clients tell me they were eating “healthy” but couldn’t lose weight, I would often find these foods in their journals. Often, they were consistently eating “healthy” foods like egg-white omelets, non-fat Greek yogurt, and soy burgers on whole-grain buns. Over time, your body can develop a reaction to those foods when you overdo it.   

Learn the best swaps for gluten in this blog. 

How to Determine Whether You Have Food Intolerance 

There are a few ways to determine whether you can’t tolerate a particular food. Dr. Pedre mentions two lab tests to identify food reactions. As your doctor for the following (or order directly here):  

  1. The radioallergosorbent (RAST) assay identifies immediate (IgE-mediated) sensitivities. 
  2. The enzyme-linked immunosorbent assay (ELISA) identifies both immediate and delayed food sensitivities.  

He notes that while neither test is perfect, ELISA is more precise in identifying specific IgG antibodies to foods. 

I talk more about food-sensitivity testing and what I learned from using them in this mindbodygreen blog. 

Honestly, I’m far more interested in the bodily response that you feel rather than what a lab test tells you. If a test says, “No, you’re fine with eating corn,” but you eat corn and feel crappy, that’s a sign you shouldn’t be eating corn. 

Keeping a food journal that includes what you eat and the symptoms that may show up hours or days later can be very helpful here.  

“The best way to tell if you are food sensitive or intolerant is to keep track of your symptoms and then eliminate that specific food,” says Pedre. 

As you keep a journal, pay attention to symptoms such as joint pain, gas and bloating, headaches, and fatigue. Craving a particular food like cheese is another surefire signal that you have food intolerance.  

While elimination diets can be helpful, I learned that many people were reacting to seven particular foods that I discuss in The Virgin Diet. When you eliminate these foods, you may find that during the first few days that they’re feeling worse than ever. That’s a sure sign that you were having a reaction to that food!  

By the end of week one when you eliminate the offending foods, however, amazing things happen. As your immune system calms down and inflammation falls in check, you look and feel better. Your joint pain is gone, your skin’s cleared up, your headaches are going away, your fatigue is gone, and you don’t have post-meal gas and bloating.  

Learn more about how to know if you have food intolerances in this episode of Ask the Health Expert. 

Final Thoughts: Address Food Intolerance with The Virgin Diet 

We really don’t know all the reasons people react negatively to food. The best test is your own body.  

“You may be consuming foods that your body has developed an immune response or sensitivity to without your even knowing it,” says Vincent Pedre, MD, in Happy Gut. “When you remove the foods that are ‘toxic’ to your body because they activate your immune response, weight loss happens naturally.” 

The simplest way to determine whether you’re reacting to these foods is to remove them for at least 21 days. I’ll guide you through the entire process in The Virgin Diet. When you eliminate these foods, you lose weight, have more energy, sleep better, have clearer skin, and miserable symptoms like gas and bloating disappear.  

Learn more and order your copy of The Virgin Diet here. 

The views in this blog by JJ Virgin should never be used as a substitute for professional medical advice. Please work with a healthcare practitioner concerning any medical problem or concern. The information here is not intended to diagnose, treat, or prevent any disease or condition. Statements contained here have not been evaluated by the Food and Drug Administration

*These statements have not been evaluated by the Food and Drug Administration. This product is not intended to diagnose, treat, cure, or prevent any disease. 


  1. https://www.nhs.uk/conditions/food-intolerance/