Nutrition

Food Intolerance vs. Allergy: Important Differences You Need to Know

Written by Dr. Chad Walding, DPT

February 26, 2025

The food we eat is supposed to provide our bodies with the fuel and building blocks it needs. But what happens when the food we eat becomes the enemy – making us feel sick and even threatening our lives?

Unfortunately, this is the reality for millions of people who suffer from food allergies or food intolerances. What’s even scarier is that food allergies and intolerances are on the rise – with more and more people being diagnosed each year.

While food allergies and food intolerances both involve a negative reaction to the foods we eat, there are some crucial differences between the two that you need to know.  

Table Of Contents

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

Since food allergies and food intolerances can have overlapping symptoms, people often confuse the two. But there are some distinct and important differences between them. 

A simplified way that many people differentiate the two is (1):

  • Food allergies involve a response from the immune system 
  • Food intolerances are a response involving the digestive tract

The human body is complex and interconnected, so this is an oversimplification of exactly how food allergies and food intolerances work. So let’s take a closer look at exactly what happens in your body when you have a food allergy or food intolerance. 

What is a Food Allergy?

Your immune system is your body's defense mechanism. It’s a complex system composed of a network of organs and cells that work together to protect and defend your body against invading substances. 

When your body detects an invader, it releases an army of chemicals, proteins, and specialized cells that target and attack the identified pathogen. This reaction is known as the immune response or an inflammatory response. 

When you have a food allergy, your body flags a certain food as a foreign invader that needs to be attacked and eliminated. This hypersensitivity leads to an exaggerated response and sends your immune system into full-blown attack mode in an attempt to rid your body of the ingested food. 

Common Food Allergies

Common Food Allergies

Any food can create an allergic reaction and is highly dependent on each individual person. But there are eight common foods that cause 90% of all documented food allergies. They are (2):

  • Milk
  • Eggs
  • Wheat
  • Soy
  • Fish
  • Shellfish
  • Peanuts
  • Tree nuts (cashews, almonds, walnuts, pistachios, etc.)

What Are the Symptoms of a Food Allergy?

The symptoms of a food allergy can be life-threatening and should be taken very seriously. The most severe form of a food allergy response is called an anaphylactic reaction or anaphylaxis (3).

When your body has an anaphylactic reaction, it has an extremely exaggerated response to the allergen – causing the immune system to go into overdrive and flood the body with chemicals that can cause the body to go into shock. Blood pressure drops and airways narrow making it a life-threatening situation.

Fortunately, anaphylactic reactions are rare. But it’s crucial to know the signs and symptoms of a food allergy because repeated exposure to a food allergen can further exaggerate the body’s immune response and eventually create an anaphylactic reaction. 

The symptoms of a food allergy may include (4):

  • Skin reactions such as hives, itching, or swelling
  • Wheezing or difficulty breathing
  • Vomiting or diarrhea
  • Swelling of the throat and tongue

Symptoms can occur within minutes of ingesting the allergen or take up to 30 minutes. If you notice any of these symptoms, it’s important to seek emergency treatment right away.

Food Allergy Testing

Pinpointing the exact foods that cause an allergic reaction is important. Sometimes, when symptoms appear within minutes of eating, this can be an easy task. But often, it requires a more in-depth approach to discover what is causing the reaction. A food allergy is often identified by using a combination of diagnostic tools including (5):

  • Keeping a food diary and logging any symptoms to check for patterns.
  • Eliminating all suspect foods for a period of at least two weeks and then slowly reintroducing them one at a time to monitor for reactions. This should be done under medical supervision and is not safe for those who have had an anaphylactic reaction.
  • A skin prick test where small drops of liquid food extract containing suspected allergens are placed on the skin. The skin is then “pricked” and monitored for a reaction, which is typically a small red bump.
  • A blood test where blood is drawn and sent to a lab where it is analyzed for indicators of a food allergy.

Food Allergy Treatment

The primary treatment for a known food allergy is to avoid coming into contact with the food entirely. Once the body has identified a particular food as an invader and created antibodies to target it, it continues to cause an immune response anytime it is ingested.

For severe food allergies, some people even have to avoid being in the same vicinity as the foods that trigger their immune response. For example, due to the rise of peanut allergies, many school lunchrooms have become “peanut-free” in an attempt to accommodate students with allergies. 

If you have an identified food allergy, it is also important to have self-injectable epinephrine available in the event of an emergency. Epinephrine is the drug administered in the event of anaphylactic shock. Having a self-injectable dose can save your life and buy you valuable time until emergency services arrive.  

What is a Food Intolerance?

A food intolerance, also known as food sensitivity, is not life-threatening and does not directly involve the immune system. Food intolerances do indirectly involve your immune system, and some, like celiac disease, are associated with an autoimmune disorder. But the difference is that intolerances do not cause the immediate and exaggerated response seen in a true allergy. 

The body’s response to a food intolerance is triggered by your body’s inability to break down something that was ingested. Some reasons your body may not be able to properly break down an ingested food may be (6, 7)

  • Lack of certain digestive enzymes that are needed to break down a certain food: Lactose intolerance, or the inability to adequately breakdown dairy is a common example.
  • Sensitivity to certain food additives: Some people’s body responds negatively to additives such as MSG, sulfites, dyes, or preservatives added to processed foods.
  • Difficulty digesting the components of certain food: For example, many people have difficulty breaking down gluten, a protein found in wheat. 
  • Inability to properly break down certain sugars: Some people are sensitive to certain naturally occurring sugars found in common foods such as onions, asparagus, Brussel sprouts, and high-fructose fruits.

Food Intolerance and Inflammation

Remember when I said food intolerances indirectly cause an immune response?

Food intolerances do not cause a full-blown and immediate immune response like an allergy. But the frequent introduction of foods your body can't properly digest creates a vicious cycle of low-grade inflammation. 

When you frequently eat food that your digestive system can’t properly break down, it can cause increased intestinal permeability, also known as leaky gut syndrome. This means that the cells that line your digestive tract become compromised and you develop tiny “gaps” between them. 

These tiny gaps then allow food particles and bacteria to “leak” out into the bloodstream. The body flags these particles and launches an immune response, causing low levels of inflammation.

This creates a vicious cycle because as inflammation increases, food intolerances worsen, causing even more damage to the intestinal lining, and allowing even more particles to leak out.

Common Food Intolerances

Your body can become intolerant to any food. But there are certain food intolerances that are seen frequently and maybe the culprit if you suspect you’re experiencing symptoms of sensitivity.

Lactose Intolerance

Lactase is an enzyme found in the digestive tract that breaks down lactose, the sugar found in milk and dairy products (8). Lactase is normally found in adequate amounts in infants and small children – likely due to their need to digest breast milk – but many adults do not maintain high enough levels of lactase to break down dairy.

Without adequate lactase, lactose passes through the body undigested and can cause significant digestive upset.

Celiac Disease

Celiac disease is often confused with a wheat allergy. But it is, in fact, an autoimmune disease. 

When someone has celiac disease, their body has an immune response to gluten and proteins found in wheat, barley, and rye (9, 10) This overreaction of the immune system can cause widespread and serious effects that impact your entire body. 

Non-Celiac Gluten Intolerance

Non-celiac gluten intolerance is similar to celiac disease in the body responds negatively to the introduction of gluten and proteins found in wheat, barley, and rye (11, 12) Tests used to confirm celiac disease only test for antibodies to a handful of components found in gluten. But there are many additional components found in gluten that can cause potential reactions

Non-celiac gluten intolerance is still not well understood but is well documented as a food intolerance that resolves when gluten is removed from the diet and aggravated when re-introduced. 

FODMAP Intolerance

FODMAP stands for fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (13). FODMAP’s are a type of carbohydrate or sugar found in certain foods such as:

  • Onions
  • Garlic
  • Beans
  • Wheat
  • Beer
  • High-fructose fruits like apples and nectarines

In FODMAP intolerance, the digestive system has difficulty breaking down these sugars, causing them to ferment in the gut which creates gas and a movement of fluid into the intestines (14). 

What Is a Delayed Food Intolerance?

Food intolerances can be tricky to pinpoint because they can show up days after ingesting the food and can have vague and unrelated symptoms. A reaction that presents a significant amount of time after ingesting said food is known as a delayed food intolerance, or more accurately identified as an IgG- or IgA- mediated food intolerance (15, 16, 17). 

So what on earth does that actually mean?

It simply means that certain foods elicit a response from the immune system that triggers the release of IgG or IgA antibodies. These are the antibodies associated with the low levels of inflammation created by frequent exposure to foods that your body can’t properly digest. 

This low-level immune response is exactly why food intolerances are difficult to identify. Because low-grade chronic inflammation impacts your entire body, not just your digestive tract. And this can cause widespread and seemingly unrelated symptoms.  

What Are the Symptoms of a Food Intolerance?

When it comes to food intolerances, the easiest symptoms to spot involve your digestive system. But since a food intolerance indirectly causes an immune response by causing inflammation, it can also cause vague symptoms that seem unrelated or aggravate other conditions. 

Some examples of symptoms that may be caused by a food intolerance include (18, 19):

  • Diarrhea
  • Constipation
  • Gas
  • Bloating
  • Nausea
  • Abdominal discomfort
  • Aggravation of autoimmune disorders such as eczema or asthma
  • Rashes
  • Headaches
  • Fatigue
  • Joint pain

In fact, many people have found that eliminating food their body has difficulty digesting can yield significant improvements to their quality of life. Low-level health concerns like IBS, frequent headaches, or fatigue often get ignored because we learn to tune them out and accept them as the norm. But sometimes addressing food intolerances can improve your health in ways you aren’t expecting since low-level inflammation can be sneaky and impact you on so many levels.

Food Intolerance Testing

Food intolerances can be particularly tricky to diagnose for a few reasons:

  • Symptoms can be vague or unrelated to each other and vary significantly from person to person.
  • Some people may be intolerant to numerous foods or certain types of foods (like FODMAPs), making it difficult to figure out which foods are to blame. 
  • There are no reliable, accurate, or validated tests for identifying food intolerances.

The gold standard when it comes to pinpointing food intolerances is the elimination diet. Foods that are known to be common intolerances, as well as any foods that may be suspect, are excluded from the diet for a minimum of two weeks (although it’s recommended to eliminate them until all symptoms have resolved). 

If symptoms begin to resolve, then it’s time to identify the culprit. Excluded foods are slowly reintroduced one by one, allowing enough time between introductions to monitor for an adverse reaction. 

Since no one knows your body better than you, this trial and error method is often the best way to gauge whether or not your unique body can tolerate certain foods.

It’s important to note that following an elimination diet is intended to be short term and used as a tool to aid in pinpointing food intolerances. An elimination diet should always be completed under the supervision of an experienced healthcare professional such as a doctor or nutritionist.

Food Intolerance Treatment

Identifying what foods cause a negative reaction and eliminating them is the simplest and most effective way to address food intolerances. Some people may even be able to tolerate trigger foods in very small amounts without having a reaction. 

Certain food intolerances, like lactose intolerance, may be able to take supplements to aid in digestion. For example, if you suffer from lactose intolerance, you can purchase a supplement that contains the enzyme lactase to help your body digest dairy. 

Many people assume that if they have a food intolerance, they are stuck with it for life. But the good news is that, unlike food allergies, you may be able to do something about a food intolerance.  

Healing Food Intolerance

Since food intolerances are caused by an inability to properly digest certain substances, they generally circle back to your overall gut health. 

Many times, addressing gut health and taking steps to heal your gut can yield impressive results when it comes to your body's ability to tolerate previously triggering foods. On top of avoiding trigger foods, here are some ways you can start healing your gut:

Take a Collagen Supplement

Collagen is a protein that essentially helps “seal the gaps” in your intestinal lining by giving your body the building blocks to heal damaged cells and grow new tissue. Look for a collagen supplement that doesn’t contain any ingredients that are commonly associated with intolerances like dairy, soy or gluten. 

Eat Fermented Foods

Fermented foods go through a process known as Lacto fermentation during which starches breakdown and create byproducts that are beneficial to your gut such as enzymes and beneficial bacteria. Fermented foods include:

  • Sauerkraut
  • Kombucha
  • Kimchi
  • Yogurt

While all of these foods are beneficial to your gut, it’s a good idea to introduce them slowly. Flooding your gut with with enzymes and flora – even the good kind – can cause unpleasant side effects like gas, bloating, or indigestion.

Restore Your Gut Flora

Your gut contains trillions of bacteria that are designed to maintain a certain balance. When you are dealing with food intolerances, leaky gut syndrome, and low-level inflammation you can bet your bottom dollar that your gut flora has become imbalanced.

An important part of healing your gut is restoring your gut flora back to it’s balanced and optimal state. Taking a probiotic formulated to repopulate your gut with the right types and amounts of microbes can give your gut the boost it needs.

Are You Struggling With Food Intolerances?

Dealing with food intolerances can be miserable. They can impact the quality of your life and even influence the longevity of your life.

Low-grade inflammation created by food intolerances affects your entire body and over time can have serious consequences. Chronic inflammation has been linked to nearly every chronic disease known to man.

But the good news is, you are not a victim or a helpless passenger when it comes to food intolerances. You have the power to give your body the tools it needs to heal and restore itself to a vibrant state of health. All you need is the right guidance to unlock the natural health that mother nature encoded each and every one of us to experience.

A New Approach To Health

Addressing the root cause of your food intolerances and any other health concerns requires a customized and comprehensive approach unique to your individual biological make-up. It requires addressing all of the facets that impact your health: 

  • The food you eat
  • The way you move your body
  • The quality of your sleep
  • The environment you spend your time in
Dr. Chad Walding
Article by

Dr. Chad Walding

Dr. Chad Walding is the Co-Founder and Chief Culture Officer at NativePath. He is a Doctor of Physical Therapy with a passion for helping people eat, move, and live in harmony with their natural state.

Read More
Share onfacebook

    Medical Disclaimer

    This content is for informational and educational purposes only. It is not intended to provide medical advice or to take the place of such advice or treatment from a personal physician. All readers/viewers of this content are advised to consult their doctors or qualified health professionals regarding specific health questions. Neither Dr. Chad Walding nor the publisher of this content takes responsibility for possible health consequences of any person or persons reading or following the information in this educational content. All viewers of this content, especially those taking prescription or over-the-counter medications, should consult their physicians before beginning any nutrition, supplement, or lifestyle program.

    Leave a Comment