Do you feel like your food intolerances are holding you back or controlling your life? Do you wish you knew how to overcome them, and to do so in a meaningful, sustainable way? That’s what I want to talk to you about today, because I know there is a better way.

In this article, we will discuss food intolerances, what separates them from allergies, and the action steps you can take to get them under control. Ultimately, you won’t have to worry about them anymore, and I’m here to help you take the first step.

That first step will often include rebuilding your good gut flora, which can be done with something like resistant starch. It’s why I put together RS Complete, to help start that process.

Do You Have Food Intolerances Or Allergies?

First, we have full-on food allergies. These are things like peanut reactions, but we also have IGA reactions (like celiac), that can come about. These are ones that we do not yet know if they can be changed, so the picture is a bit unclear there.

Then, there are food intolerances. These are the ways in which certain foods simply do not make you feel well. Maybe it showed up on a test, or maybe it did not, but either way it is having a real effect on your ability to enjoy certain foods or ingredients.

Key Insight: If there are foods that are affecting you, it is critical to know that and to be able to identify them. Then, you can work around those foods.

So, how do we go about resolving this issue rather than simply living with it?

Here’s something that might not be all that intuitive. When there are digestive problems that cause food intolerances, if you do not address the problem you may find yourself intolerant to more and more things.

There can even be a point where, because your diet is so limited, that by itself is hurting your gut flora and digestive function. This makes you reactive to more and more foods, which is the opposite intent of avoiding certain foods in the first place!

How Do Food Intolerances Happen?

There can be neurological ways that food intolerances can come about, involving cytokines, histamine reactions, but there can also be expectations at play. Fear itself is powerful, and it can also have a very real effect on digestive function.

That in mind, all of these mechanisms are ones that do not happen to everyone. Let’s think about that: While many people are exposed to histamines in their diet, they are not reactive. The trick is to be aware of what your body is sensitive to and address it.

My Personal Experience With Food Intolerances

This is a topic that is definitely meaningful for me. After all, I went through a very similar experience that I would love to share with you.

In the first phase, I went through the process of cutting out a lot of junk food and sugar, and did quite well. I added in protein and exercise, and it revealed itself to be quite helpful.

Later on in my life, though, I had another chapter in my life in which I became highly restrictive. I stumbled on some books that were becoming popular at the time, and I thought it might be a good idea to try cutting more and more things out of my diet.

This meant cutting out a whole host of natural foods that were potentially harmful (according to these books). The argument seemed compelling to me, and I did feel much better in the first few weeks or so. But, things changed and I started noticing that:

  • My physical performance
  • The ability of my body to recover
  • My mental focus
  • Overall mood
  • Food cravings

It took a long time to unravel all of these things. The first reaction was to continue along with this model, and to blame these things on what I was still eating (rather than what I cut out).

As I cut out more and more and more, it got to the point where I was eating little more than raw fruits and vegetables (once daily and not even fruit sometimes). That simply does not sustain a young person, much less anyone else.

While I did eventually figure it out, it took some time. That’s why I want to help you out today with what I have learned, and what science tells us.

The Phenomenon of Nocebo

Here’s something I want to share with you: Have you ever heard of nocebo? It’s the opposite of a placebo, and is basically something that can’t hurt you, does hurt you, because you believe that it will. As I mentioned before, I was very deep in these kinds of reactions to foods.

How Should We Start Thinking About Food Intolerances?

In general, when there are legitimate reactions to foods, we need to think about symptoms including:

  • Bloating
  • Migraine
  • Fatigue
  • General aches and pains

Especially when they are digestive in nature, these can be significant. There is the thought that such reactions can worsen immunity and trigger thyroid disease. While I have heard about it, I haven’t seen the evidence to back it up.

For sure there has been data that people with thyroid disease have higher amounts of food intolerances, but not the other way around. Is the thing that causes thyroid disease also causing food reactions? Or, are the food reactions causing thyroid disease?

The best-studied examples we have are from those suffering from celiac disease. In those cases, it is very clear that those with thyroid disease have more celiac disease (and vice versa)1.

Four Steps To Overcoming Food Intolerances

Here are the five steps that you can take to start healing your food intolerances and reversing them completely, naturally!

Step 1: Identify and Avoid

This is the first big step when it comes to healing food intolerances naturally. You need to figure out what makes you reactive!

If you have things triggering your immune system, which you might be ingesting on a daily basis, you are never going to give your body the chance to calm down. So, figuring out these culprits is the first step.

That said, identifying your food intolerances is not going to be an intuitive process. Someone with celiac disease might be totally fine eating wheat, in the sense that they do not notice any symptoms.

But, they still may be increasing their risk for:

  • Colorectal cancer
  • Malabsorption
  • Immune distress

A symptom diary might also be tempting. But, the problem here is that symptoms might take days, or even weeks, before you feel them. And, you may never end up noticing them!

It would also have to include staving off certain foods, or keeping off large groups of foods all at once, so that you can really get a good idea of what is causing you to react. Simply put, it just isn’t practical.

Key Insight: We can’t rely on our subjective sense of how well we feel after we eat certain foods. That’s why it definitely is not the way to find out or discover our food intolerances.

In fact, some of the reactions we may face from different foods could take days or weeks before they do anything at all.

The best place to start is to test, not guess! And, the best tests to help identify food intolerances include IgG and IgG4 antibodies2.

From my experience, some of the most accurate labs include:

  • KBMO – a food inflammation test
  • Meridian Valley
  • US Biotek

Of course, it still takes the skills of a qualified doctor, who knows IgG to know if these are things you’re reactive to or tolerant of — because, based on food allergy tests, it may look the same to some.

In order to reset and move past your reaction, I would have to say that full avoidance and commitment is crucial.

It is definitely not easy, but it is the best way to help heal your food intolerances naturally.

Bottom Line: Once you know what you are reactive to, through testing, you are going to want to do your best to avoid those foods entirely. This means no quantity at all for a known block of time (3 – 6 months). 

While it might seem like a long time, it is so important when you are looking to get better long-term. Not simply to “feel better” in the short term.

Step 2: Treat Chronic Infections

Let’s talk about our flora! As you avoid certain foods, you need to also make sense of any “bad bugs” that you might be carrying in your system. Then, you can treat them effectively.

I am always a fan of knowing more about what you are dealing with, so testing is almost always the right call. This way, you can really get a good sense of what is going on in your body.

Some of the common infections that you might be dealing with could be:

  • H.pylori – You can find out more with breath tests, blood tests, stool tests – all of these can work for initial diagnosis
  • Yeast – aA stool culture or a skin test
  • Other pathogens – Stool cultures, Doctor’s Data Stool Micro and other good tests are available to learn more about other pathogens your body might be carrying

You can also presumptively cleanse yourself of any of the bad stuff with antimicrobial treatments. There are both conventional and natural versions, which prevent parasites, viruses, fungi, and bacteria.

Bottom Line: Whether presumptively or selectively, either of these options work when it comes to treating any chronic infections you might be dealing with.

Step 3: Rebuild Flora

If you have been following the first two steps, you are already going to be well on track to rebuilding your flora.

But, let’s take things a step further! After all, we want our flora to become even stronger than before.

There are four facets that we think about when it comes to rebuilding gut flora:

  • Prebiotic foods
  • Fermented foods
  • Polysaccharides
  • Supplements

Prebiotic foods

Prebiotic foods essentially amount to a lot of plant foods, from as many categories as possible. If we go by category, we should think about:

  • Beans (kidney, black, pinto)
  • Peas (chickpeas, peas, lentils)
  • Intact whole grains
  • Vegetables and fruits
  • Nuts and seeds

In this category, prebiotic foods are going to move the needle the most for our gut flora. Of those, resistant starch is going to be the largest (Read More: My complete guide to resistant starch).

More than anything else, resistant starch is going to act as the fuel to get those good bugs in you again.

Fermented Foods

Fermented foods act as really nice adjuncts to rebuilding and preserving your good gut flora.

Some examples include:

  • Kimchi
  • Sauerkraut
  • Fermented vegetables
  • Kombucha (a little bit of debate on this one)


This is where we want to think about adding things in to help repair the intestinal tract.

Polysaccharides are a great way of helping rebuild our gut flora and you can easily think about them as ‘slimy’ foods.

You can find them in:

  • Onions
  • Cabbage
  • Okra
  • Eggplant
  • Aloe gels
  • Supplements

The ingredients you might want to look for from supplements are:

  • Glutamine3
  • NAG4
  • Quercetin5
  • DGL6

What Are Some Common Pitfalls?

When we think about getting all of these foods into our system, the problem is that it’s way too easy to not take enough of them. Or, to not take them regularly or for long enough.

And, if your digestive system is off, you may encounter symptoms by radically changing your diet. The trick here is to ensure any changes are gentle, while fast enough to make real change.

Think about some of the highest priority foods we listed, and then think about which ones you have the best tolerance of right now. Start there, and then work your way through the rest.

Of course, you should also identify the ones that do cause symptoms, too. I’m not talking about your ‘triggers,’ but think about some of the food categories that can help your flora.

Then, make a plan to phase some of those back into your diet. Some foods are gentler than others, like lentils, for instance.

Key Insight: When it comes to phasing foods in, that can be as much as a tablespoon a day. That’s really all it takes to shift your flora!

Step 4: Desensitize

What does it mean to desensitize?

Sublingual immunotherapy for foods has been shown to work even for the most dangerous allergies, like peanut allergies7,8.

This should become commercially available within the coming years, but it is not available for the public just yet. I won’t address those here today.

This is a system that works by exposing your immune system to tiny, controlled doses of the reactive item. So, here’s a technique that I have guided countless amounts of people through to help them safely reverse their food intolerances at home.

Healing Your Food Intolerance Naturally

As always, make sure you check with your own health care provider before trying anything new – and know that you cannot use this technique for any anaphylactic reactions like nuts, shrimp, or other shellfish.

Also, many foods cause reactions for reasons that are not based on your immune system – these other types of reactions may not improve through desensitizing.

Basically, what you are going to be doing is making an oral sublingual dilution at home with every food that is reactive for you. This is not going to be helpful for things that are inherently hard on your body, like processed sugars, preservatives or flavorings.

We also have no reason to think this would work for those with long-standing wheat reactions such as celiac disease.

Informal Desensitizing

Think about the categories of plant foods like:

  • Vegetables
    • Cruciferous (broccoli, cabbage, kale)
    • Allium (onions, garlic, leeks, scallions)
    • Greens (spinach, collards, dark lettuce)
    • Starchy (squash, sweet potato, white potato)
  • Fruits
    • Berries
    • Citrus
    • Stone fruit (peaches, apricots)
    • Apples
    • Tropical (banana, manago, papaya)
  • Nuts
  • Seeds
  • Beans (black beans, pinto beans, lentils)
  • Peas (chickpeas, green peas, black-eyed peas)
  • Intact whole grains

The more of these categories that you can include regularly, the more robust and diverse your gut flora will be. We now know that it is not about always raising any one type of flora as it is about trying to have many different types together.

Formal Desensitizing

There are also steps you can take at home that are more precise. They can often bring about similar benefits as medical desensitization.

The steps are simple:

  1. Choose your top three reactive foods (dairy, eggs, or almonds, for example)
  2. Measure one gram of a cooked version of each food, with a food scale (for under $10 you can find a great scale that can measure to 0.1 grams)2
  3. Add 1 liter of purified water
  4. Blend in a high-powered blender for two minutes. This is now a 1/1000 dilution of your allergen and it contains 0.001 grams of it
  5. Place in glass container and store in the refrigerator for three days
  6. Buy glass milliliter measuring dropper10
  7. Take 1 milliliter of mixture twice daily and hold under tongue for one minute
  8. Make a fresh batch every three days

After One Month: Repeat the same process with 100 ml of water (roughly 3 ounces). This is now a 1/100 dilution of your allergen and it contains 0.01 grams of it.

After Two Months: Repeat the same process with 10 ml of water (roughly 1/3 ounce). This is now a 1/10 dilution of your allergen and it contains 0.1 grams of it.

Finally, you will want to start testing 1/2 servings of your reactive foods (on alternating days). If no obvious symptoms emerge, reintroduce gradually and keep monitoring symptoms.

Heal Your Food Intolerances Today

Food intolerances are really serious. They can have a major impact on your health and on your life.

The last thing we want to do is worsen our overall health based on the things we eat, because it is so easy to control what we eat and to get the healthy foods we need to feel good.

Thankfully, you do not have to be stuck with food intolerances long-term. If you follow these five steps, you are going to do so much for your body to naturally reverse your food intolerances.

It takes time, but it can be so easy, and it relies on your body’s own amazing ability to heal itself. Change is always possible, we just need to make sure that it is a good change.

Heal Your Intolerances, Heal Your Thyroid

Food intolerances can have a major effect on your thyroid and we all know how important your thyroid is in governing your overall health. Do you know the state of yours?

Take the thyroid quiz today (Click Here: Take the quiz today) and learn a little bit more about your health and how you can go about feeling your best.


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P.S. Whenever you are ready, here is how I can help you now:

1. Schedule a Thyroid Second Opinion with me, Dr. C, Click Here for Details
2. Download and use my Favorite Recipes Cookbook Here
3. Check out my podcast Medical Myths, Legends, and Fairytales Here

Dr. Alan Glen Christianson (Dr. C) is a Naturopathic Endocrinologist and the author of The NY Times bestselling Adrenal Reset Diet, The Metabolism Reset Diet and The Thyroid Reset Diet.

Dr. C’s gift for figuring out what really works has helped hundreds of thousands of people reverse thyroid disease, lose weight, diabetes, and regain energy. Learn more about the surprising story that started his quest.