The Top Food Intolerance Symptoms Of Hidden Food Sensitivities

The Power of Adaptogens from a Functional Medicine Expert Dr. Will Cole

Food is medicine, and yet, food can also be one of the biggest contributors to chronic health problems. Our bodies are alive because of the way the foods we eat either feed health or feed disease. You may think you already know this. No sugar and junk food, obviously, right? But food triggers can be much more subtle than fast-food French fries and supersized sodas.

Much of your individual body’s reactions to the foods you eat come from your unique biochemistry, microbiome configuration, lifestyle, stress level, and immune status. I have seen the healthiest foods flare up food intolerance symptoms in one person, contributing to inflammation in their muscles and joints, digestive problems, and brain fog, while the next person can thrive on those same foods. How can the same food be good medicine for one person and bad medicine for another? I see three primary causes for this apparent discrepancy:

Food allergies: True food allergies come from an immediate and severe reaction of the immune system to some aspect of a particular food. Symptoms of an allergic reaction can include rashes, itching, hives, and swelling, or even anaphylaxis, which involves swelling of the airways and difficulty breathing which can be fatal.

Food intolerances: Unlike allergies, these do not directly involve the immune system. Instead, intolerances occur when your body is unable to digest certain foods (such as dairy) or when your digestive system becomes irritated by them. These are usually the result of enzyme deficiencies.

Food sensitivities: These are similar to intolerances, but it’s often less clear why someone reacts poorly to a certain food. Food sensitivities may result in a more delayed reaction, and you might be able to digest a small amount of the food without issues.

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However, for some, continually ingesting a food that they are sensitive to can cause long-term chronic health issues they may have no idea are linked to a food sensitivity. Symptoms might include:

  • Acid reflux/heartburn
  • Anxiety
  • Arthritis
  • Bloating
  • Brain fog
  • Constipation
  • Chronic fatigue syndrome
  • Diarrhea
  • Eczema
  • Fatigue
  • IBS (irritable bowel syndrome)
  • Headaches/migraines
  • Hives
  • Inflammation
  • Itching
  • Joint pain
  • Mood swings
  • Muscle pain
  • Nausea
  • Rashes and other skin problems
  • Sinus infections
  • Stomach cramps
  • Weight gain
  • Weight loss
  • Wheezing

As Hippocrates says “All disease begins in the gut.” A weak microbiome can lead to increased inflammation and in turn, a cascade of other health problems – food intolerances and sensitivities included. For example, when your gut is compromised, like in leaky gut syndrome, foods end up passing through the gut lining into the bloodstream. This can put your immune system in overdrive and lead to increased inflammation throughout your body. With this hyper-awareness, your immune system ends up reacting to almost any food that passes through, including healthy foods like spinach.

The Inflammation Spectrum

Leaky gut syndrome and other conditions are really just the end scale of a larger inflammation spectrum. This spectrum can be broken down into three stages:

  1. Silent autoimmunity: There are no symptoms but there are positive antibody labs.
  2. Autoimmune reactivity: When there are symptoms as well as positive antibody labs.
  3. Autoimmune disease: When there’s enough body destruction to be diagnosed with a specific condition.

For example, the autoimmune condition celiac disease, is ultimately the end stage (1) of gluten sensitivity. About 10 percent of people with celiac disease have noticeable digestive symptoms but still deal with other symptoms like acne. Because of this, only about 5 percent (2) of true celiacs are actually diagnosed leaving about 20 percent of people unknowingly struggling with gluten intolerance.

How To Start Healing

From eating gluten just one time, it can take almost 6 months (3) to bring down autoimmune-inflammation antibodies. This is a big deal! There are multiple factors that can influence gut health such as inflammatory foods, stress, and medications therefore a lot needs to be considered when it comes into healing the digestive system. While I usually see monthly improvements in my patients it takes a full two years before dramatic and sustainable changes happen. It takes the average adult gut between 18 to 24 months to completely heal. Remember, this is a journey, not a race. It took years to get to this point of destruction and will also take time to repair.

Around 80 percent (4) of your immune system is located in your gut. It only makes sense then that by healing your gut could bring relief to food sensitivities. Now, that doesn’t mean that every person and every food sensitivity will be completely healed forever – but it doesn’t have to be a life sentence!

1. Get lab work done

To begin the healing process, it’s important to find your baseline. If you think food sensitivities are a problem for you, labs will help determine both the cause and specific sensitivity. This will allow you to make sure you’re addressing everything necessary for healing. Here are the just a few of the labs that I run for patients at my functional medicine clinic:

  • Microbiome labs: This will show you whether or not you have a bacterial imbalance and if you need to boost your good bacteria. Research has shown that imbalances can dysregulate (5) the immune system and contribute to food sensitivities.
  • Small intestinal bacterial overgrowth: SIBO occurs when bacteria overgrows up from the large intestines into the small intestines. This bacteria ends up eating the foods you eat and will ferment in the wrong area leading to gas, bloating, and if untreated, leaky gut syndrome.
  • Leaky gut labs: These blood tests will measure antibody levels to show if there has been damage to the gut lining.
  • Zonulin and occludin: These two proteins control gut permeability. Antibodies indicate damage to intestinal tight junctions.
  • Actomyosin: This shows if there has been destruction of gut lining.
  • Lipopolysaccharides: Antibodies to these these bacterial endotoxins in your gut can indicate leaky gut syndrome.
  • Histamine intolerance: During an allergic reaction your body releases chemicals known as histamines. This is a normal part of a healthy immune system. Certain foods naturally contain histamine or trigger the release of histamine. Some people though, can have an overload of histamine due to a deficiency or dysfunction of the enzymes that break down histamine. This is known as histamine intolerance. It can create what is called a “pseudoallergy,” – an allergic reaction without an allergen.

2. Try an elimination diet

This is my gold standard tool for discovering food sensitivities. Removing certain foods for a period of time and then slowly reintroducing them will reduce inflammation, give your gut a healing break, and will give you insight into which foods cause a reaction for you.

3. Make sure to rotate your food

Eating a variety of vegetables, meats, and fruits will give your body a diverse range of nutrients and will also keep your immune system balanced as you start to reintroduce certain foods.

4. Amp up your gut healing

If you don’t work on healing your gut, it doesn’t matter how many elimination diets you do. Ultimately you’ll be left fighting the same symptoms over and over. Once you have discovered which foods you need to be eliminating (at least for the time being), you can begin to incorporate these next-level gut healers:

  • Bone broth: This soothing food medicine will bring healing to damaged gut lining.
  • Probiotics: Supplements in addition to natural probiotics like fermented foods (think kimchi and sauerkraut) will restore any imbalances in your microbiome by bringing good bacteria into your gut.
  • Intermittent fasting: I often see great success with this functional medicine tool in my clinic. When you go for short periods of time without eating, you give your digestion a much-needed rest.
  • Cooked foods: By eating only cooked foods you decrease the amount of work your digestive system needs to do to break the food down.

So, once you have worked on your gut health you may find that certain problem foods are now tolerable. However, it is important to remember that certain foods are naturally inflammatory so even though you can handle them, it’s good to still only eat them in moderation.

What about At-Home Testing?

As more people become educated about the importance of health, do-it-yourself wellness has risen in popularity, and lab testing is one important way to figure out the cause of health issues on your own. In the age of Amazon and instant access to almost anything from the convenience of your home, lab tests offer a multitude of at-home food sensitivity tests, each one claiming to shed light on your individual food sensitivities with one simple test—they advertise no doctor’s visit or complicated elimination diet needed. However, food reactivity testing is a mixed bag and not all tests are the same—also, your results may not be as straightforward as they seem.

How at-home testing works

When you find a test you want to try, place your order. A kit will be delivered straight to your home. Each kit will vary slightly, but generally they contain detailed instructions and the necessary instruments to complete the test. These results are gained through blood analysis, so a finger prick is required to conduct the tests. By looking at your levels of IgG antibodies to particular foods (immune reaction or reactivity), these tests are able to detect even low levels of IgG activity to determine which foods could be causing problems for you. These are the most common tests on the market.

Pinner Test

Food Intolerance Test ($380): This test looks at your response to 200 foods, making it one of the most comprehensive at-home kits on the market.


Food Sensitivity Test ($159): This test is less comprehensive than the Pinner Test as it looks at your response to only 96 foods but it is also less expensive. You do have the option to upgrade to the Food Sensitivity Expansion Test, which will test an additional 88 foods.

Food Sensitivity+ ($249.99): This option not only looks at your body’s response to different foods, but it takes it a step further and looks at the relationship your DNA has to your ability to digest certain foods such as caffeine.

Cash Labs

Food Sensitivity Test ($199): Like EverlyWell, this test looks at 96 foods.

Do home tests work?

Each test presents the results in its own way, but in general, you will receive a list of foods that the test has determined are causing some level of reactivity in your system. You could just quit eating the foods on the list, but many people want a professional to help them with what to do next, especially when the list of reactive foods is long. When prospective patients send me their at-home food sensitivity lab results and I see numerous food reactivities, it often tells me that the problem isn’t necessarily a legitimate sensitivity to every single food on the list, but an overall lack of gut health and an overreaction of the immune system to many foods that may not be a problem when your body is less inflamed and aggravated.

In my experience, when patients retake these tests months later, they may get different results because labs are snapshots in time. If your health and lifestyle have changed, your results are likely to change, too. The results for any lab, food sensitivity labs included, are looking at the specific day and time that the lab specimen was collected. Life and health are dynamic, so on any given day, your immune system could be behaving differently and reacting differently to different foods. And in the case of someone with multiple food sensitivities, their immune system is even more likely to have ups, downs, twists, and turns, depending on the day in the short term, and changes in health over the long term.

So what do you do if your results reveal many food sensitivities? This is when I recommend rotating the foods you eat, to keep your immune system more calmed and balanced by avoiding eating one food too often. My goal as a functional medicine practitioner is not to have patients just avoid every food that shows a positive reaction in a test, but to treat the underlying issues causing the sensitivities to flare up. Depending on how many foods are positive, I may have patients limit or avoid those foods for a time while actively working on healing the underlying gut-immune problems that are causing the reactions in the first place. Also, I recommend actively working on improving your gut health – this is generally a good idea anyway, but it can certainly help to reduce immune system reactivity. Later, when health improves, chances are good that many of the foods on that long list can be successfully re-introduced.

Another thing to consider is how you will respond to your test results. If you see that you have numerous food sensitivities detected by an at-home test kit, will this lead to more stress and anxiety for you? Will you worry that you can’t eat anything but air and ice cubes? Stress and anxiety are not good for gut health, or health in general! For some people, labs like these without a qualified functional medicine doctor or coach can fuel food anxiety and eating problems like orthorexia, so if this feels like something you’d be predisposed to, I’d recommend avoiding them.

Who should take these at-home tests?

DIY food testing labs can provide you with a good, base-level window into how your immune system is reacting to foods. If you can’t or don’t want to work with a functional medicine practitioner right now, I see these labs as beneficial for people who have tried healing their guts on their own but feel like they aren’t getting anywhere or are stuck at a plateau, or for people who have already cleaned up their diets but are still having some symptoms. Information about specific foods to avoid for a while can jumpstart your healing. A direct-to-consumer microbiome test like Viome can add further information. Together with food tests, they can give you a good overall look at the landscape of microbiome.

Bottom line: These tests can still give you enough information to start cleaning up your diet, even if you aren’t yet ready to consult a professional.

The Most Common Food Intolerances and Sensitivities

Here are the foods that I find most commonly cause problems for my patients:

1. Gluten-containing grains: wheat, rye, barley

Gluten, the protein that’s found in grains like wheat, rye, and barley, is probably one of the most common sensitivities that I see. If you do a little research, you may discover that according to estimates, approximately 18 million Americans have a “gluten sensitivity.”

Is gluten intolerance real?

Not everyone agrees yet, but an increasing number of doctors and scientists are saying yes. One trial (6) published in Clinical Gastroenterology and Hepatology studied people who thought gluten was causing them digestive problems. The gold standard for research is something called a randomized, double-blind, placebo-controlled, crossover trial, and gluten was put to this rigorous test.

For one week, participants were given either a small amount of gluten or a placeo pill of rice starch. After only one week, those who were taking the gluten pills reported a significant increase in symptoms compared to those who took gluten-free placebo pills.

Another recent randomized control trial shared similar findings. (7) These studies are good evidence that some people do experience uncomfortable side effects after eating gluten. More research is ongoing, and I expect that as the concept of gluten intolerance continues to gain credence, we will see even more reputable research legitimizing this condition.

Is gluten intolerance an autoimmune condition?

To understand gluten intolerance, we need to understand autoimmune conditions. Many people think when we talk about gluten intolerance we are referring to the autoimmune condition celiac disease. Yes, celiac is an autoimmune disease, but it is the extreme end of a broader gluten-intolerance spectrum. (8)

You can be on the autoimmune-inflammation spectrum without having celiac disease, and that can result in gluten intolerance, or what doctors sometimes call non-celiac gluten sensitivity (NCGS). You may not have tests that come back saying you have an autoimmune disease, but I believe that gluten reactivity is a warning that you could eventually be headed in that direction if you don’t change your diet and health habits.

What are the symptoms of gluten intolerance?

People in the study experienced:

  • abdominal bloating
  • ulcers
  • intestinal pain

Because your gut is your “second brain,” people with gluten intolerance can also experience:

  • brain fog
  • depression
  • anxiety
  • fatigue

If you believe you might have a sensitivity to gluten, there are some tests you can consider.

You can get tested for celiac disease, but assessing gluten tolerance is a little more difficult. Mention gluten, and a conventional doctor will likely get a simple alpha gliadin lab. If it comes back negative, you are told you don’t have celiac disease. However, not everyone with celiac disease has a positive alpha gliadin test. There are more tests that can be done. A functional medicine doctor can also perform even more tests to assess gluten reactivity. Alpha gliadin and the common celiac lab Transglutaminase 2 are just two pieces of about a 24-piece puzzle.

On top of all that, some people react to other aspects of wheat gluten – in fact, there are about 24 different qualities in wheat that can cause reactivity. More comprehensive labs could be incredibly helpful for someone who needs motivation to eliminate some or all grains, or for someone who has reintroduced grains into their diet but is still unsure whether grains are problematic for them.

Gluten Cross-Reactive Labs:

Yet another layer to the problem of gluten intolerance is cross-reactivity. This is when foods that do not contain gluten are “tagged” with gluten antibodies, so that the body reacts to them as if they are gluten, often due to a similar molecular structure. Like a case of mistaken identity this case of mistaken identity can wreak havoc on the person who has gone gluten-free but still has symptoms. Some cross-reactive foods may include:

  • gluten-free grains
  • milk/dairy products
  • soy
  • coffee
  • chocolate
  • eggs

2. Gluten-free grains: corn, rice, buckweat

Those who choose to avoid gluten but are still having symptoms may not realize that they are grain-intolerant, even when those grains are gluten-free. If this sounds like you, then know that you could have a sensitivity to any particular grain, or all grains. Or, your problem might be cross-reactivity, in which the proteins in grains such as rice and corn can be similar enough in structure to gluten that the body mistakes them and reacts as if they were gluten. This is called molecular mimicry and is sort of like a case of mistaken identity. Many of my patients have sensitivities to some gluten-free grains, although not all.

3. Nightshades

A plant group that consists of tomatoes, peppers, potatoes, eggplant, goji berries, and some spices containing alkaloids, which can be inflammatory for some people.

4. Alcohol

Regular consumption of alcohol can potentially negatively influence almost every system in your body. For the gastrointestinal system in particular, alcohol can be a trigger for leaky gut syndrome and gut inflammation in some people.

5. Sugar

Obvious, right? But do you know why? Sugar is the favorite food of more pathogenic gut bacteria that can cause many gastrointestinal problems, so when you eat sugar, you are feeding the bad guys so they can crowd out the good guys that do nice things for you. An imbalance of bacteria (9) in your gut can also lead to negative effects on your body’s metabolism and immune responses, and overgrowth of bad (sugar-loving) bacteria can also cause inflammation, which can eventually lead to an autoimmune-inflammatory response. Don’t think artificial sweeteners are the answer, though – research shows that they also decrease (10) the good bacteria in the gut, which could also cause glucose intolerance and lead to diabetes.

6. Legumes

Legumes include all types of beans (kidney, garbanzo, black, fava,) lentils, peanuts, edamame, and soy products (tofu, miso.) Many of these foods are staples for people who are trying to eat more plant-based meals, but the lectins and phytate proteins of legumes can be hard for some people to digest. The carbohydrates are also yummy food for your gut bacteria, and when they consume them, they release gas, which means you get gas and the accompanying bloating and discomfort.

Even if you don’t get gas from legumes, they could cause undue stress to your gastrointestinal and immune system due to those lectins and phytates. Peanuts might also contain aflatoxin (toxins produced by a mold), while soy has phytoestrogens, which can interfere with healthy hormone balance. Of all the legumes I have found that soy tends to be the most likely to cause problems for people.

7. Eggs

The incredible egg has many nutrients, mainly in the yolk, but that doesn’t mean it isn’t problematic for some. In my experience, it is actually the egg white that is typically more immunoreactive for people. The protein in the white, albumin, could pass through the intestinal lining if you have leaky gut syndrome, contributing to inflammation. The yolks are generally better tolerated, although it’s important to note that some people can’t handle the yolk, either.


This strange sounding acronym stands for Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols. In short: fermentable sugars. These short-chain sugars are contained in many different foods and are not fully digested in the gut, which can cause them to be excessively fermented by gut bacteria.

This fermentation releases hydrogen gas that could lead to distension of the intestines, which can cause uncomfortable IBS symptoms in some people, such as pain, gas, bloating, constipation, and diarrhea. This would be considered a FODMAP intolerance, and tends to be related to functional issues like small intestinal bacterial overgrowth (SIBO.)

Most of the high-FODMAP foods are actually healthy whole, foods, but again, that doesn’t mean they work well for everyone. If you think you are FODMAP intolerance, try avoiding or severely limiting the following foods, at least temporarily, to see if it helps:


Artichokes, asparagus, beetroot, celery, garlic, onions, leek bulb, legumes, Savoy cabbage, sugar snap peas, sweet corn


Apples, mango, nectarines, peaches, pears, plums, watermelon


Milk, cream, custard, ice cream, soft cheeses, yogurt


Rye, wheat-containing breads, cereals, crackers, pasta


Cashews, pistachios

Fructose, one FODMAP sugar, is one of the more common intolerances. Fructose intolerance (11) is often found in people with recurring stomach pain and bloating. The goal with treating a FODMAP intolerance is not to remove the foods forever but to heal the gut so that you can eventually increase your intake of these foods, especially the high-FODMAP fruits and vegetables, which are valuable sources of nutrients.

9. Dairy

Casein, a protein found in animal milk and products made from it like ice cream and cheese, is another common sensitivity. But there is more to the dairy story. Cows on most major dairy farms are routinely given hormones to increase milk production and antibiotics to combat mastitis infections. They also tend to live in unhealthy, unclean conditions, and are fed corn instead of their natrual food, grass. Their milk is then typically pasteurized (super heated) and homogenized (blended) and the fat is often removed. To make up for this highly processed product having so little remaining nutrition, synthetic vitamins are typically added back into milk, in an attempt to simulate what nature had already included in the first place, in its whole-food form.

Organic dairy is better because it does not allow the use of hormones and antibiotics. Fermented dairy, such as grass-fed kefir and yogurt, is even better, as it mitigates some of the problems people have with casein sensitivity and includes beneficial bacteria, so it may be better tolerated. However, some people can not ever have any dairy, in any form.

10. Nuts and seeds

The roughage of nuts and seeds, and well as the lectin and phytate proteins, can irritate some people’s digestion. Plus, most nuts sold in stores are typically coated in inflammatory industrial seed oils, like soybean or canola oil. They could also contain partially hydrogenated trans-fats, which can contribute even more to inflammation. I find that people who are intolerant to nuts typically do better buying them raw, soaking them, and lightly toasting them at home. I also recommend enjoying them sparingly.

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  1. Sapone A, Bai JC, Ciacci C, et al. Spectrum of gluten-related disorders: consensus on new nomenclature and classification. BMC Med. 2012;10:13. Published 2012 Feb 7. doi:10.1186/1741-7015-10-13
  2. Lohi S, Mustalahti K, Kaukinen K, et al. Increasing prevalence of coeliac disease over time. Aliment Pharmacol Ther. 2007;26(9):1217‐1225. doi:10.1111/j.1365-2036.2007.03502.x
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  8. Sapone A, Bai JC, Ciacci C, et al. Spectrum of gluten-related disorders: consensus on new nomenclature and classification. BMC Med. 2012;10:13. Published 2012 Feb 7. doi:10.1186/1741-7015-10-13
  9. Payne AN, Chassard C, Lacroix C. Gut microbial adaptation to dietary consumption of fructose, artificial sweeteners and sugar alcohols: implications for host-microbe interactions contributing to obesity. Obes Rev. 2012;13(9):799‐809. doi:10.1111/j.1467-789X.2012.01009.x
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Dr. Will Cole, DNM, IFMCP, DC is a leading functional medicine expert who consults people around the globe, starting one of the first functional medicine telehealth centers in the world. Named one of the top 50 functional and integrative doctors in the nation, Dr. Will Cole provides a functional medicine approach for thyroid issues, autoimmune conditions, hormonal imbalances, digestive disorders, and brain problems. He is the host of the popular The Art Of Being Well podcast and the New York Times bestselling author of Intuitive Fasting, Ketotarian, The Inflammation Spectrum and the brand new book Gut Feelings: Healing the Shame-Fueled Relationship Between What You Eat and How You Feel.

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