Hashimoto’s Flare Up Triggers: 9 Common Causes Explained

Hashimoto’s Flare Up Triggers: 9 Common Causes Explained

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Problems With Your Immune System Leads to Hashimoto’s Flare-Ups

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There are two very important things you should always remember if you have Hashimoto’s:

#1. Hashimoto’s is primarily a disease of your immune system.

Yes, Hashimoto’s can and does cause thyroid problems but it is the immune aspect upstream which triggers all of the problems downstream. 

Because of this, you should always be thinking and asking yourself about how well your immune system is working. 

And #2. Hashimoto’s is a dynamic disease, not a static one.

Put in simple terms, Hashimoto’s is a disease that will ebb and flow

In this case, the ebbs of Hashimoto’s mean that your disease state is under control and that you aren’t destroying your own thyroid gland (which is the hallmark of Hashimoto’s). 

When your Hashimoto’s is flowing that is a bad sign and an indication that you are in what we call a Hashimoto’s flare-up. 

A Hashimoto’s flare-up is a flare-up of your immune system which then triggers a cascade of problems in the thyroid gland. 

As your immune system flares up it results in damage to the thyroid gland which alters how much thyroid hormone is being produced. 

This leads to all sorts of symptoms that can range from mild to severe on the thyroid spectrum. 

The entire goal in someone with Hashimoto’s is to put your disease state into a permanent ebb (in other words, put it into remission). 

To do that you need to focus on avoiding things that make your Hashimoto’s worse. 

And that’s exactly what we are going to be discussing today.

In this article, you will learn:

  • The most common triggers of a Hashimoto’s flare up
  • How to avoid these triggers so you can keep your Hashimoto’s under control
  • What to do if you are experiencing a flare-up (how to stop it)
  • And much more…


Foods to Avoid if you Have Thyroid Problems:

I’ve found that these 10 foods cause the most problems for thyroid patients. Learn which foods you should avoid if you have thyroid disease of any type.


The Complete List of Thyroid Lab tests:

The list includes optimal ranges, normal ranges, and the complete list of tests you need to diagnose and manage thyroid disease correctly!


9 Of the Most Common Triggers of Hashimoto’s Flare-Ups

As you read through these triggers you will find that they all have one thing in common:

They all impact your immune system!

#1. Your Diet (The Most Triggering Food Groups)

Yes, we pretty much always need to have a discussion about diet whenever we discuss managing the thyroid. 


Because diet is something that you have complete control over. 

You get to control what type of food you put into your mouth. 

You get to control what types of foods don’t make it into your mouth. 

And you get to control how much you are eating. 

This isn’t true of a lot of other therapies, such as thyroid medication, which your doctor is in complete (usually) control over. 

It shouldn’t surprise you that the food that you put into your mouth has a potentially huge impact on both thyroid function as well as immune function. 

If you wanted to (heaven forbid) sabotage your thyroid then here’s what you would do:

  • Eat lots of foods with gluten, dairy, and soy – Many patients with Hashimoto’s have sensitivities to all three! Simply avoiding dairy has been shown to improve thyroid lab tests (1) in some women with Hashimoto’s. Soy can cause problems with thyroid function and gluten can be damaging to the gut lining. 
  • Eat lots of refined and processed carbohydrates – Refined and processed carbohydrates can interfere with insulin levels and lead to inflammation (2)
  • Eat lots of processed foods – Processed foods are devoid of the nutrients that your thyroid needs, they are calorically dense, and contain artificial chemicals and preservatives that have no place in your body. 
  • Consume plenty of inflammatory and industrial seed oils – Industrial seed oils are high in omega-6 fatty acids which push down on the inflammation gas pedal. 
  • Avoid foods that are high in omega 3 fatty acids while favoring foods high in omega 6 fatty acids – You want to achieve a balance between omega 3 fatty acids and omega 6 fatty acids. This is why consuming healthy fats such as salmon, fish, nuts, and seeds, are all beneficial for those with Hashimoto’s. 
  • Avoid fruits and vegetables as much as possible – Fruits and vegetables contain important phytochemicals, vitamins, and minerals that your thyroid needs to function optimally! 

Unfortunately, most of the foods that you will find at a grocery store fit into the categories above. 

So if you are someone with Hashimoto’s that really isn’t paying attention to the foods that you put into your mouth or if you don’t fully understand how to read a nutrition label, then it’s time to make some changes!

Changing your diet has the potential to send positive signals to your hormones, brain, and gut, which can then act to change immune function as well as inflammatory pathways in the body. 

Think of the food that you put into your body as information. 

You want that information to tell your immune system to reduce inflammation and stop attacking your thyroid gland. 

You do not want that information to tell your immune system to flare up, cause inflammation, or damage your thyroid. 

You can read more about the various types of diets that actually are helpful for those with Hashimoto’s here

#2. Emotional and Physical Stress

Any type of stress perceived by your body can result in a flare-up of Hashimoto’s but the two that I want to focus on here include:

  • Physical stress – Physical stress is something that has physically impacted your body. This could be from trauma (like a car accident) but would also include things like an illness or even too much physical exercise. 
  • And Emotional stress – Emotional stress is a type of stress that you can’t see but one that is still felt by the body. Stressors in this category may include things like worry, fear, anxiety, sadness, or other emotional responses that you experience each day. 

Stress is one of those things that is severely underappreciated by doctors and patients alike. 

Stress has the ability to negatively impact just about every aspect of your physiology ranging from your hormones to your immune system. 

Constant exposure to stressful situations puts pressure on your adrenal glands which produce cortisol. 

Issues with cortisol can then cause thyroid problems directly. 

High levels of stress can also suppress your immune system (3) which will make you more likely to get sick when exposed to common bugs and viruses. 

I’ve found stress to be a significant and important trigger of both Hashimoto’s itself as well as Hashimoto’s flare-ups. 

Based on my experience, here are some of the most common stressful situations that may lead to a flare-up: 

  • Death of a loved one
  • Acting as a caregiver for a loved one for an extended period of time
  • Problems with your spouse or with a relationship
  • Divorce
  • Issues relating to your children (problems at school or issues with friends)

Women with Hashimoto’s tend to be very giving with their time and energy, so much so that it can often be the trigger of the disease itself or a flare-up. 

Pay attention to your stress and do things that can not only reduce your stress but help you become more resilient to stressful situations. 

#3. Viral Infections (Acute or Chronic)

Emerging evidence suggests that certain viruses play an important role in triggering the Hashimoto’s disease state. 

I’m not talking about a flare-up here, I’m talking about causing the entire disease. 

Common viruses known to have an association include EBV (4) as well as CMV (5).  

These are two well-known viruses by the Hashimoto’s community because case studies suggest that treating these viruses may actually help put Hashimoto’s into remission. 

There’s evidence to suggest that this may be true, but even if it isn’t, we still care about viruses because of their impact on your immune system more generally. 

When you are sick with a virus your immune system is under more pressure to take care of and kill it.

This very act requires energy and puts stress on the system. 

Any stress on the immune system will make you more vulnerable to Hashimoto’s flare-ups. 

Any illness of any type has the potential to lead to a flare-up because of this. 

This doesn’t mean that every time you get sick you will get a flare up, though. 

In fact, that’s usually not the case. 

People who have a balanced immune system and are not suffering from other issues, such as physical or emotional stress, or who are eating a healthy whole food diet, will be able to handle infections much better than someone who is not doing those things. 

The viruses I mentioned above (EBV and CMV) are more sinister compared to viruses like the flu because these viruses stay with you for life. 

Once you get infected with them your body puts them into remission but is never completely able to eradicate them. 

As a result, these viruses can rear their ugly heads when your immune system gets compromised from stress, unhealthy eating, or a lack of sleep. 

Because these viruses have been known to trigger Hashimoto’s, it’s plausible that when they recur they could then trigger a flare up via a similar mechanism. 

The same sort of thing happens when someone gets shingles from stress. 

Shingles are just a reactivation of chickenpox (6) that decided to come out in the form of shingles when the immune system couldn’t keep it under control. 

By maintaining a healthy immune system you can not only prevent future infections but also prevent reactivation of certain viruses that may trigger flare ups. 

#4. Nutrient and Vitamin Deficiencies

Vitamins and nutrients play an important role in regulating your immune system as well as thyroid function. 

This connection is so strong that certain nutrient deficiencies increase your risk of developing autoimmune disease (I’m looking at you vitamin D). 

Those with Hashimoto’s are at increased risk for developing nutrient deficiencies because of how the thyroid impacts gut health. 

Low thyroid function (as seen in Hashimoto’s) decreases stomach acid production and alters bowel motility. 

Both of these set up a situation in which absorbing nutrients can be difficult for thyroid patients. 

The result?

A higher risk of nutrient deficiencies impacts both the immune system as well as your thyroid. 

Not all nutrients are important for your immune system so I have highlighted some below that you will want to pay close attention to. 

It is always a good idea to double-check on these nutrients if you are in a flare or if you just aren’t feeling 100%: 

  • Zinc and Selenium – We can’t talk about the thyroid and vitamins without mentioning both zinc and selenium. Both zinc and selenium are important for thyroid function but they also play protective roles in the body as it relates to Hashimoto’s. Zinc, for instance, is necessary for healthy immune function (7) and selenium helps to protect the thyroid gland (8) from thyroid gland inflammation. In addition, both of these vitamins help your body convert T4 into T3 (the active thyroid hormone). 
  • Iodine – Iodine is a controversial topic, especially when it comes to Hashimoto’s. There’s no doubt that iodine can cause issues in those who have thyroid autoimmunity but these problems stem from incorrect usage of iodine (not the iodine itself). Both excessively high doses of iodine, as well as complete avoidance of iodine, may trigger Hashimoto’s and lead to flare ups. The best thing you can do is find what I call the Goldilocks zone of iodine intake which is a daily dose somewhere between 150 and 250mcg. Iodine is both safe and effective for those who have Hashimoto’s as long as it is used correctly! 
  • Vitamin D – Vitamin D deficiency is a huge problem in the world with deficiency rates as high as 30%. This is a big problem because we know that vitamin D deficiency increases your risk of developing autoimmune diseases (9) like Hashimoto’s. One of the first things you should do as a patient newly diagnosed with Hashimoto’s is to both check your vitamin D level and optimize it with vitamin D supplements if necessary. Vitamin D3 supplements (not D2) are very effective at increasing Vitamin D status in the body and can be purchased over the counter. If you are not getting out in the sun regularly then there is a very high chance you are deficient. 
  • Magnesium – We know that people who have magnesium deficiency are more likely to develop Hashimoto’s as well as thyroid problems. We also know that stress depletes magnesium stores in the body! Because of this, if you are not actively paying attention to your magnesium intake then there is a good chance you are not getting enough. 
  • Antioxidants – Antioxidants play a protective role in those with Hashimoto’s because they can help protect the thyroid gland from thyroid gland damage. The hallmark of Hashimoto’s is thyroid gland inflammation which ultimately leads to thyroid gland destruction. Free radicals are a natural byproduct of thyroid gland production in the thyroid and must be neutralized by antioxidants to protect against damage. Those who have Hashimoto’s often do not have enough antioxidants to combat these free radicals which leads to more damage. Because of this, supplements such as vitamin A, C, and E may help protect the thyroid gland when taken in patients with Hashimoto’s. 

#5. Bacterial Infections (Acute or Recurrent)

Just like viral infections, bacterial infections can put stress on the immune system and may lead to a Hashimoto’s flare up. 

Much like the viruses we mentioned previously, some of these infections may also cause or trigger Hashimoto’s in those who don’t already have it. 

In addition, once you have some of these infections they may recur and lead to flare ups after diagnosis. 

These bacteria have been known to cause issues for those with Hashimoto’s: 

  • H. Pylori – Short for Helicobacter Pylori, this little bug is what causes stomach ulcers. H. pylori sets up shop inside the lining of your stomach which leads to damage and inflammation in the gut. It’s not exactly clear why H. pylori infections are associated with Hashimoto’s thyroiditis but it’s felt to be related to the fact that both of these organs originate in the foregut during development (10). Because of this, they share similarities in how the tissue is organized. Whether this makes them susceptible to the same disease, we aren’t sure but we do know that there is a connection. H. pylori infections can both cause Hashimoto’s as well as flare-ups. If you are someone who has Hashimoto’s of unknown origin then it would be a good idea to get your gut checked to see if you have this bug! Some cases of H. pylori can go undetected unless tested for. 
  • Yersinia enterocolitica – Yersinia is found in undercooked pork and isn’t very common in developed countries but it can be associated with flare-ups (11). 
  • Borrelia burgdorferi – This is the bug behind Lyme disease (12) which is an incredibly difficult to treat infection. Lyme disease isn’t very common but it’s more common than most people realize. 
  • Any other bacterial infection – Lastly, virtually any other infection can put a strain on your body and lead to a scenario in which a flare-up is more likely. Minor bacterial infections such as strep throat or a sinus infection can temporarily weaken your immune system and set the stage for a future flare-up. 

#6. Lack of Sleep & Lack of Exercise

I’ve added these here to illustrate the compounding effect that multiple stressors can have on your body. 

It’s not like forgetting to exercise a few times or having a couple of bad nights of sleep will cause a flare-up but instead, it’s usually a combination of things that stack on top of each other to create the perfect storm. 

Think about it like this:

Imagine a scenario in which you are under a lot of stress. 

This stress could be because you are acting as a caretaker for someone you love or because of pressure at work or because of relationship issues with your spouse. 

This stress is now significant enough to cause you some anxiety. 

Now because you are having a little anxiety you aren’t sleeping as well as you used to. 

Now because you aren’t sleeping very well you don’t have enough energy to exercise as regularly as you used to. 

Now because you aren’t sleeping well you don’t have the energy or time to cook your meals so you are eating out more. 

Now because you are eating out more you aren’t getting the nutrients that you used to. 

All of a sudden this small stressor in your life has triggered a cascade of events that has multiplied and you now have 4 or 5 potential triggers for a Hashimoto’s flare up. 

This is pretty much how it works in the real world and this sort of scenario is what I see most often. 

It’s not one single thing that causes it, it’s the combination of everything stacking on top of each other. 

And sometimes the thing that triggers it all is something simple like stress, lack of sleep, or not exercising. 

Make sense? 

When it comes to sleep you can think about it as one of the best things that you can do for your body. 

Missing just a few hours of sleep is enough to change your mood, lower your sex hormones, impact your thyroid, and alter your immune system. 

The same goes for exercise. 

Regular daily exercise has been shown to result in protective benefits to your immune system. 

#7. Parasites

Just like bacteria and viruses, some parasites can also trigger flare ups. 

While big and systemic parasites are uncommon in developed countries, there are some types of infections that can lead to flare ups and perhaps even trigger Hashimoto’s. 

One in particular worth mentioning is blastocystis hominis. 

There have been some case reports (13) linking Hashimoto’s to blastocystis hominis infections. 

These case reports also suggest that treating the underlying infection may lead to a positive impact on Hashimoto’s and may even allow for reversal of symptoms. 

The best way to test for blastocystis hominis is with a stool microbiologic exam. 

#8. Exposure to Endocrine Disrupting Chemicals

Next up we have exposure to endocrine disrupting chemicals or EDC’s for short. 

EDC’s include a range of different types of chemicals that have hormone-disrupting properties (hence the name!). 

These chemicals act by either blocking your native hormones or by mimicking these hormones at the cellular level. 

They’ve also been shown to interfere with thyroid lab tests (14) by making your thyroid lab tests look better than they actually are. 

Chemicals in this group include:

You may just assume that you don’t have to worry about these chemicals because you think you aren’t coming into contact with them. 

Unfortunately, if you are thinking that then you’d be wrong!

These chemicals are found in plastics, on receipts, in drinking water, in lotions/creams, and many other places. 

Even if you are actively trying to avoid them you will still come into contact with them to some degree. 

For most people, though, this isn’t a huge deal. 

The body has built-in systems designed to get rid of toxins and can eliminate them through the stool and urine. 

That is all well and good but it makes one major assumption:

That those systems are working properly. 

And this isn’t always true for patients with thyroid disease. 

Let’s look at gut function as an example. 

What happens if you have low thyroid function? It leads to constipation. 

Do you think you are going to be as effective as another person with regular bowel movements if you can’t eliminate toxins through your stool?

The answer is obviously no. 

Something like chronic constipation can slowly lead to a build-up of these endocrine disrupters which can set the stage for a Hashimoto’s flare up. 

Because of this, it’s always a good idea to make sure you are doing basic things to ensure that your detoxification systems are working optimally. 

Ensuring that you are sweating on a weekly basis, drinking enough water, and making sure you have at least one bowel movement per day are easy ways to do this. 

#9. Increased Intestinal Permeability (Leaky Gut)

Lastly, we need to talk about increased intestinal permeability (20) otherwise known as leaky gut. 

Don’t let the name confuse you, when we are talking about increased intestinal permeability and leaky gut what we are really talking about is damage to the intestinal lining of the gut. 

This intestinal lining is important because it’s the barrier that protects the inside of your body from whatever enters into your gastrointestinal tract. 

It’s designed to prevent the things that you don’t want to get into your body ,to not get in, and to allow the things that you do want to get in, to get in. 

For instance, you want certain nutrients, vitamins, minerals, and even food to get absorbed and you don’t want chemicals, portions of bacteria, plastics, etc. to get inside of your body. 

Normally, this intestinal lining works to do just that. 

Unless you have a leaky gut. 

If you have a leaky gut then that protective barrier is not so protective and things may start to enter into your body that you don’t want to get in. 

As this happens you may start to experience inflammation in the gut and even trigger an immune response in the body, both of which can lead to a Hashimoto’s flare up. 

Leaky gut isn’t the only gut problem that may lead to a flare up. 

In fact, there are many others. 

Some of these include:

For these reasons, paying attention to your gut is always important if you are someone who has Hashimoto’s. 

Some of these gut conditions can be treated with simple things like changing up your diet and taking a couple of supplements. 

Others may require the use of more powerful herbal antibiotics and antifungals or even prescription antibiotics and antifungals. 

Wrapping it Up

As someone with Hashimoto’s, it’s important to have a basic understanding of a Hashimoto’s flare up. 

I’ve listed 9 of the most common triggers of Hashimoto’s flare ups but there are certainly others out there! 

As you navigate through your disease you may find that you are more susceptible to certain triggers while others tend to not bother your body and immune system as much. 

That’s okay. 

What matters most is figuring out what triggers a flare up in your body and avoiding or treating that thing. 

Doing this will ensure that you keep your Hashimoto’s symptoms under control and give you the best possible shot at either reversing your condition or managing it. 

Now I want to hear from you:

Were you aware of these triggers?

Have you experienced a Hashimoto’s flare up before?

If so, what do you think triggered it? Were you able to identify that trigger and fix it?

Are you planning on getting tested for any of these potential triggers?

Let me know in the comments section below! 

#1. https://pubmed.ncbi.nlm.nih.gov/24078411/

#2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6139832/

#3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2790771/

#4. https://pubmed.ncbi.nlm.nih.gov/25931043/

#5. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5704440/

#6. https://www.cdc.gov/shingles/about/transmission.html

#7. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5748737/

#8. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5307254/

#9. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6047889/

#10. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167994/

#11. https://pubmed.ncbi.nlm.nih.gov/12193307/

#12. https://pubmed.ncbi.nlm.nih.gov/16571084/

#13. https://pubmed.ncbi.nlm.nih.gov/26230132/

#14. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5751186/

#15. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1241914/

#16. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6165121/

#17. https://pubmed.ncbi.nlm.nih.gov/9549759/

#18. https://pubmed.ncbi.nlm.nih.gov/12414890/

#19. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5638801/

#20. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5988153/

what triggers a hashimoto's flare up?

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About Dr. Westin Childs

Hey! I'm Westin Childs D.O. (former Osteopathic Physician). I don't practice medicine anymore and instead specialize in helping people like YOU who have thyroid problems, hormone imbalances, and weight loss resistance. I love to write and share what I've learned over the years. I also happen to formulate the best supplements on the market (well, at least in my opinion!) and I'm proud to say that over 80,000+ people have used them over the last 7 years. You can read more about my own personal health journey and why I am so passionate about what I do.

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