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The Elimination Diet And Thyroid Health

When taking a natural treatment approach it of course is important to eat a healthy diet.  Although most endocrinologists dismiss dietary factors as playing a role in thyroid or autoimmune thyroid conditions, the truth is that eating a lot of refined foods and fast food on a frequent basis can lead to many different health issues.  However, some people don’t improve even when eating a healthy diet, and while it’s possible that there can be other factors affecting their health (i.e. stress, lack of sleep, an infection, toxins, etc.), in order to achieve optimal health it is important to avoid eating any foods you might be reacting to.

An obvious question you might have is “what foods should I eliminate?”  Not surprisingly you will get different opinions from different healthcare professionals.  But most will agree that the most common allergens should be eliminated, along with a few other foods.  This includes gluten, dairy, corn, eggs, soy, shellfish, peanuts, and refined sugar.  And because most refined foods and fast food include one or more of these allergens it is best to stick with eating whole foods while on an elimination diet.  Some healthcare professionals will also recommend avoiding foods such as beef, pork, coffee, tea, citrus fruits, and chocolate during an elimination diet.

An Elimination Diet For Those With Autoimmune Thyroid Conditions

Many people reading this are familiar with the autoimmune paleo diet.  This recommends for people to avoid most of the common allergens I listed above (gluten, dairy, corn, eggs, soy, peanuts, refined sugar, coffee), but also recommends avoiding legumes, nuts and seeds, along with the nightshade vegetables.  This of course makes the diet even more challenging to follow, but because legumes, nuts, seeds, and the nightshades have compounds which can potentially increase the permeability of the gut it probably is a good idea for most people with Graves’ Disease and Hashimoto’s Thyroiditis to avoid these foods.

I do think following an autoimmune paleo diet as an elimination diet is a good idea for many people with Graves’ Disease and Hashimoto’s Thyroiditis.  And of course those who do well with this diet can choose to continue following it until their health has been restored back to normal.  However, there are a few issues with this diet.  One problem is that it’s a very restrictive diet, as it essentially allows the person to only eat vegetables, fruits, lean meats and fish, coconut products, and some healthy oils (i.e. coconut oil).  Even with these restrictions many people are able to follow such a diet, especially on a short term basis, although it can be very challenging.  This is true for most people, but it is especially true for vegans and vegetarians.  And regardless of whether someone eats meat or not, some people don’t do well on an autoimmune paleo diet, even when it’s followed for a short period of time.

The other dilemma is that it is possible for people to have an allergy or sensitivity to one of the “allowed” foods.  In other words, someone might be sensitive to chicken, avocados, or kale, which are all permitted on an autoimmune paleo diet.  While these sensitivities are much less common, it still is possible to be sensitive to these and other foods.  Of course one can do food allergy and/or sensitivity testing, but this can get expensive, and the accuracy of such tests is controversial.  Research shows that the ALCAT testing is controversial (1) [1], and although I have done IgG testing in the past, it’s not something I do on everyone, mainly because they are very expensive tests and I still question whether such testing is completely accurate.  I do like the new Multiple Food Immune Reactivity Screen from Cyrex Labs, although this test is also very expensive and has some limitations.

What I personally do is have most of my patients follow a strict autoimmune paleo diet initially, and then after the first month if they are struggling I’m usually open to them reintroducing some foods that typically aren’t allowed.  For example, eggs aren’t typically allowed on an autoimmune paleo diet, and I discussed the reason behind this in my blog post entitled ” Can People With Graves’ Disease and Hashimoto’s Thyroiditis Safely Eat Eggs? [2] “.  But many people do fine eating eggs, especially the egg yolks, and in most cases, those who don’t do well will experience some symptoms upon reintroducing eggs.  Although nuts, seeds, and grains (even gluten free) are also not part of an autoimmune paleo diet, there are some people who choose to reintroduce small amounts of these foods and have no problems.  On the other hand, there are also people who reintroduce these foods and don’t do well, and eventually need to eliminate them from their diet again.

Below I have listed some of the main foods I recommend to be avoided initially, and I also include which ones are allowed when following an elimination diet for those with thyroid and autoimmune thyroid conditions.  Once again, I realize this can be very challenging for many people, and in the next post I’ll discuss reintroducing foods.

FOODS WHICH SHOULD BE AVOIDED:                                           




Grains (even gluten free)





Refined sugar








Vegetables (excluding the nightshades)

Fruits (some elimination diets recommend to avoid citrus fruits)

Poultry (chicken, turkey, etc.)


Other Meat

Wild fish low in mercury and other toxins

Some coconut products (i.e. unsweetened coconut milk and yogurt)

Healthy oils: olive oil, coconut oil

If you want a more complete list of the foods that are allowed and “forbidden” on an autoimmune paleo diet I would recommend reading the book “The Paleo Approach” by Sarah Ballantyne.  In this book she gives some comprehensive lists regarding the foods you can and can’t eat.  Although beef and pork are allowed on an autoimmune paleo diet, some elimination diets exclude these foods.  And while I didn’t discuss the quality of these foods, you of course want to try eating organic whenever possible, consider eating pasture-raised eggs and poultry, and if you eat beef then choose 100% grass fed.

Obviously if you have a known allergy or sensitivity to one of the “allowed” foods then I would avoid it.  Also, even though I listed coconut products here, keep in mind that many coconut products sold in health food stores have other added ingredients that might cause health issues (i.e. carrageenan).  As a result, if you are going to eat coconut products such as coconut milk and/or coconut yogurt during the elimination diet it is best to make your own.

How Long Should You Follow An Elimination Diet For?

You want to follow such a diet for at least three or four weeks.  The reason for this is because the antibodies take at least three weeks to significantly decrease.  So for example, if someone has a sensitivity to eggs and eliminates them for only one week, this won’t be a sufficient amount of time to reduce the antibodies, and thus the person who is sensitive to eggs probably won’t notice a difference upon reintroducing them.  On the other hand, after approximately three weeks of eliminating eggs the antibodies should greatly decrease, and so if the person with an egg sensitivity reintroduces eggs they most likely will experience some negative symptoms.  As a result, after three or four weeks most people can begin reintroducing some foods, which I will discuss in the next blog post.

Will You Experience Any Negative Symptoms While On The Diet?

Some people do experience negative symptoms when initially beginning an elimination diet.  These symptoms can include fatigue, headaches, lightheadedness, and gastrointestinal symptoms.  These symptoms usually only last for a few days, and not everyone experiences them.

Can I Expect Any Improvement In My Symptoms?

While some people experience a worsening of symptoms initially, many notice an improvement in their symptoms after a few days or a few weeks.  Some of the common symptomatic improvements reported by those following an elimination diet include an increase in energy, a decrease in brain fog, better sleep, a decrease in gastrointestinal symptoms, and a decrease in pain.  Keep in mind that just because you’re not noticing an improvement in certain symptoms doesn’t mean that you’re not benefiting from the elimination diet.  For example, you might have low energy levels and/or sleep issues due to weak adrenals and HPA axis dysregulation, and while eliminating certain foods might help to reduce inflammation, going on an elimination diet alone usually won’t restore the health of the adrenals.  Similarly, if someone has a leaky gut due to an infection such as H. Pylori, just following an elimination diet isn’t going to help with this.

Based on what I just said you might ask the question “why not just do some testing first to see if someone has problems with the adrenals, a leaky gut, an infection, etc?”  Although I do some testing initially, what you need to keep in mind is that it is common for someone to have more than one health issue.  And sometimes it can be challenging to know what is specifically triggering one’s condition.  For example, someone might have a leaky gut that was caused by chronic stress or an infection, but they might also have a food sensitivity such as dairy that is contributing to their gut inflammation.  And so the obvious goal would be to address all factors which can cause gut inflammation and thus is preventing the leaky gut from healing.

Is It Okay To Cheat Once Or Twice During The Elimination Diet?

While many people follow an elimination diet without a problem, for others it is a big challenge.  And it’s not uncommon for someone to ask me if they are able to cheat while following it.  Or sometimes they won’t ask me, but instead will send an email letting me know that they strayed from the diet.  For example, someone might be following an elimination diet and then have a piece of birthday cake to celebrate a family member’s birthday (or their own birthday).  Or they might have been invited to a wedding and ate some foods they weren’t supposed to eat.  Or perhaps they planned the elimination diet around the holiday season and they were invited to a party where it was almost impossible to strictly follow this diet.

Cheating even once can be an issue if you the food you consume has an ingredient you are sensitive to.  And one of the main reasons for following an elimination diet is to try to determine which foods you might react to.  As a result, you really do want to be 100% compliant during this time.  The best thing you can do is to plan ahead, as if there is a special occasion where you know you won’t be fully compliant and you can’t change your plans, then postpone the elimination diet if necessary.  For example, if you have a vacation planned in a couple of weeks, then it probably is best to hold off on following the elimination diet until after the vacation.  If there is a party or another special event coming up soon that you need to attend and you don’t think you will be fully compliant with the elimination diet, then wait until after the party is over with.

Do You Really Need To Stop Drinking Coffee?

Many of my patients find it difficult to give up drinking coffee.  It’s common for someone to say that they can strictly follow the elimination diet, but they can’t give up their coffee!  I know it isn’t easy for some people to stop drinking coffee, even if it’s only on a temporary basis.  And while some people do fine drinking coffee, not everyone does okay, which is why it’s a good idea to eliminate the coffee for at least three weeks, and preferably longer than this.  I realize that some people have problems going cold turkey, and so what you might need to do first is to gradually reduce the amount of coffee you drink until you have weaned off.  For example, if you drink three cups of coffee per day then perhaps you can reduce it to two cups per day for one or two weeks, and then cut it down to one cup/day for one or two weeks until you have weaned off of the coffee.  Another option is to drink half caffeinated and half decaffeinated coffee (organic preferred), and then after one or two weeks make it 3/4 decaffeinated and 1/4 caffeinated, and then once you are drinking decaffeinated coffee it should be much easier to wean off of it.

What are the potential consequences if you continue to drink coffee?  As I briefly mentioned earlier, some people do fine drinking coffee.  But the same can also be said for other foods that are eliminated.  Some people do fine with dairy, eggs, gluten free grains, etc.  The truth is that many people do much better when eliminating the coffee.  Obviously if you have a sensitivity to coffee then continuing to drink it can be a problem.  But even if you don’t have a sensitivity, if you have adrenal issues then drinking coffee usually isn’t a good idea.  And so if you choose to follow an elimination diet please try to do your best to eliminate the coffee, even if it means taking a few weeks to wean off of it before starting the elimination diet.

Remember That The Goal Isn’t To Restrict Calories

Some people think that the primary goal of an elimination diet is to lose weight, and they not only avoid the “forbidden” foods, but limit their consumption of the “allowed” foods.  Even if your main goal is to lose weight, restricting calories isn’t the best method of accomplishing this.  While it is common for people to lose weight while following the elimination diet, the main goal is to find out which foods you might be sensitive to.  And so you don’t need to restrict the amount of foods on the “allowed” list.

Should You Continue Taking Nutritional Supplements and Herbs?

In many cases I’ve had patients take certain nutritional supplements and herbs while following an elimination diet.  However, feel free to take a break from your supplements and herbs during this time, and if someone has a lot of known sensitivities it probably is best to avoid most supplements and herbs during an elimination diet.  After all, there is always the possibility that someone can be sensitive to one or more of the supplements they are taking.  Sometimes it’s not the actual nutrient or herb that they’re sensitive to, but one of the other ingredients (i.e. fillers, gums, etc.).  This of course can also be true with medication, as someone might be having gut inflammation due to the synthetic ingredients in the one or more of the prescription drugs they’re taking.  Obviously I’m not suggesting for people to stop taking their medication while doing an elimination diet, but this is something to keep in mind.

Should Everyone With Graves’ Disease and Hashimoto’s Thyroiditis Follow An Elimination Diet?

Although I think most people with an autoimmune thyroid condition can benefit from following an elimination diet, this doesn’t mean that everyone needs to do this in order to receive good results when following a natural treatment protocol.  Not all of my patients have followed an elimination diet, but those people who are experiencing symptoms such as gastrointestinal discomfort (bloating, gas, increased or decreased bowel movements, etc.), severe fatigue, headaches, muscle and/or joint pain, and other moderate to severe symptoms not related to their thyroid hormone imbalance should consider following an elimination diet.  Once again, this doesn’t mean that a food sensitivity is definitely the cause of these symptoms, but if a food sensitivity is the culprit then obviously this needs to be detected and then removed.

Other Important Tips

In order the get the most benefits from your elimination diet there are a few other things I would recommend.  First of all, I would try to eat as many organic foods as you can.  The main reason is because there are less toxins in organic food, and in some cases someone will have a negative reaction not because of the food itself, but because of a specific toxin.  For example, someone might feel lousy at times when eating non-organic apples, but at other times might be fine.  And while they might assume they have a sensitivity to apples, the problem could be due to the high amount of pesticides found on non-organic apples.

You also want to drink plenty of water each day.  Drink purified water, or a good quality spring water out of a glass bottle.  Try to get sufficient sleep each night.  Of course there are many people who have sleep issues and therefore have problems falling and/or staying asleep.  But there are also many people who fall asleep fine but intentionally stay up much later than they should.  This isn’t too big of a deal if done on an occasional basis, but you obviously want to get a good amount of sleep on a regular basis.  Some light exercise is usually fine, but you don’t want to exercise excessively, as this is common, and too much exercise can do more harm than good.

In summary, going on an elimination diet can help to determine which foods you have a negative reaction to.  Although taking this approach isn’t 100% reliable, the same is true with other methods such as food sensitivity testing, and of course an elimination diet is much more cost effective, although it does admittedly take time and discipline.  When I recommend an elimination diet to my patients with Graves’ Disease and Hashimoto’s Thyroiditis, I essentially have them follow an autoimmune paleo diet for three or four weeks before reintroducing certain foods.  I realize this makes the diet very restrictive, but doing so is essential in some cases, and after three or four weeks most people can start reintroducing some other foods.  Please remember that you don’t want to restrict calories while following an elimination diet, and you also should try eating as many organic foods as you can, drink plenty of water, get sufficient sleep, and not exercise excessively during this time.