How Acid Reflux Drives Hashimoto’s (and Vice Versa) and How to Take the Wheel Back

There may be times when your Hashimoto’s Disease just makes you sick to your stomach. But could it actually be causing you digestive upset?

Thyroid imbalances and digestive disorders like acid reflux and GERD have a direct connection that may not be obvious but is certainly common.

If you are someone who suffers from Hashimoto’s and also finds yourself struggling with reflux regularly, you may have wondered if they were related.

The short answer is yes, but the good news is that as you work on improving one problem, you may find the other resolving itself as well.

First, it’s important to understand the difference between terms often used interchangeably (like GERD and acid reflux) and what is exactly happening when you experience them.

And then of course, how this relates to your thyroid.

Digestion Disorder Basics

As you eat, food travels down your esophagus and into your stomach. In order to keep anything from going back up, there is a sphincter at the junction of the esophagus and stomach that closes up, called the lower esophageal sphincter (LES).

The LES is triggered to close by the release of stomach acid, which has been triggered by food.

When the stomach acid doesn’t do this job, some of the acid can get up and into the esophagus, causing a burning feeling.

The Difference Between Acid Reflux and GERD

Acid reflux is the experience of having that stomach acid make its way past the LES.

But it doesn’t describe a condition because it may happen once or it may happen chronically, which are very different things.

GERD, or gastroesophageal reflux disease, is that chronic form that occurs more than just occasionally and over a longer period of time. Some doctors look for the experience to occur at least twice a week before a GERD diagnosis.

In addition to the discomfort it can cause, the long-term effects of GERD can include esophageal cancer.

What Acid Reflux Feels Like

People often have very different ways of describing how acid reflux feels because the experience can vary person to person.

As you may already know, heartburn has nothing to do with your heart.

It is actually acid reflux but the sensation happens in the general area around your heart at the base of your esophagus.

It may range from a slight warming to a burning sensation and may go all the way up the throat.

But some people suffer from GERD for years without actually experiencing heartburn, making it harder to diagnose.

The Symptoms of Acid Reflux and GERD

Besides heartburn, other symptoms of acid reflux and GERD include:

  • Sore throat
  • Hoarse voice or laryngitis
  • Chest pain
  • Chronic cough
  • Difficulty swallowing
  • Regurgitation of food or sour liquid in your mouth

Many people have their symptoms come up often at nighttime or soon after eating.

The Causes of Acid Reflux and GERD

There are a number of causes and risk factors for acid reflux and GERD, some of which you may have control over and some you may not.

The LES can naturally weaken, especially as we age, making acid reflux much more common. Lying down too soon after eating can exacerbate this.

Obesity and pregnancy increase risk because they cause pushing into the organs.

Smoking is also a risk factor.

A Main Factor of GERD: Low Stomach Acid

Perhaps the most common cause of GERD is one that is often misunderstood and is the opposite of what people expect.

Because acid reflux is caused by stomach acid, people often think that excess acid in the stomach is to blame when really the opposite is the real culprit.

If you remember, the LES is triggered by stomach acid, so when there is too little stomach acid and the sphincter doesn’t close, this is when you get acid reflux and eventually GERD.

When we turn to medications and even over-the-counter solutions, too often we are just lowering stomach acid more.

This can help temporarily but doesn’t get to the root of the problem, which leads us to take higher and higher dosages of the same medicine.

There are certainly plenty of cases of acid reflux occurring from too much stomach acid but this is actually the minority of cases.

What Does Acid Reflux Have To Do With Hashimoto’s?

So the question we return to is what is the connection between GERD and Hashimoto’s Disease?

The answer comes down to that low stomach acid and how it relates to the thyroid.

Hypochlorhydria, the term for low stomach acid, can be caused by a number of things, including natural aging and certain medications. Poor diet is also a huge factor.

But among the many roles of the thyroid is one that may surprise you: stomach acid production. This is because the thyroid regulates metabolism and slow metabolism means less stomach acid.

But while digestion may rely on thyroid activity, it goes the other way around as well. As with many organs, systems and glands in the body, the gut and the thyroid work very synergistically together.

The thyroid secretes an inactive form of a thyroid hormone called thyroxine (T4) that must be converted to an active form, triiodothyronine (T3).

The gut plays an active role on this process by supplying necessary nutrients for the conversion.

Other chemicals found in the gut may inhibit thyroid-stimulating hormone (TSH), which has the important job of triggering the production of thyroid hormones.

This means that keeping your gut flora balanced may help regulate thyroid hormone levels.

Thyroid hormones (both T4 and T3) have also been found to help prevent stress ulcers.

The Role of Autoimmunity

Anyone who suffers from Hashimoto’s is also at higher risk for a secondary autoimmune disorder, such as Celiac or rheumatoid arthritis.

The immune system may even attack the parietal cells of the stomach lining leading to less production of stomach acid.

H. pylori and Hashimoto’s

H. pylori, a bacteria that is often found in the gut, can easily become overrun and is a very common cause of low stomach acid. This lower stomach acid allows the H. pylori to take over even more.

Hashimoto’s is known to be triggered by an overabundance of H. pylori and those who have Hashimoto’s are more likely to test positive for the bacteria.

Medications May Make GERD Worse

Unfortunately, there are many doctors who still may not understand the root cause of GERD and their patients end up being put on proton pump inhibitors (PPIs).

The most common of these are Prilosec, Nexium and Prevacid. Their job is to reduce stomach acid, which they do very well.

And in the short-term, this can cause some relief since it stops the reflux.

But if the true problem is LOW stomach acid, the result is that the patient needs higher and higher dosages to combat the fact that the LES is not being triggered anymore.

Even if you’re not taking PPIs, your medication may be affecting your GERD or your GERD could even be affecting your medications.

Levothyroxine is a commonly prescribed thyroid replacement medication.

But GERD has been found to inhibit the absorption of levothyroxine, possibly requiring higher dosage.

There are a number of other medications known to increase the risk of GERD or GERD symptoms, including antibiotics (which are often used to combat H. pylori), iron supplements, ibuprofen and aspirin, opioids, progesterone and statins.

Progesterone, a steroid, is also produced naturally by women (and men in lower amounts).

Some women may experience GERD during peak progesterone times like during pregnancy, PMS and perimenopause.

Foods That Trigger Acid Reflux

If you’ve ever experienced acid reflux more than once, you’ve probably noticed there are some foods that may trigger it more than others.

While this can vary person to person, some foods that may cause acid reflux include:

  • Gluten (both gluten sensitivity and Celiac have a strong connection to Hashimoto’s)
  • Tomatoes
  • Coffee and black tea
  • Dairy (a common food intolerance)
  • Soda
  • Citrus
  • Alcohol
  • Raw onion or garlic
  • Chocolate

You may have heard about taking apple cider vinegar for acid reflux.

This is an excellent food that is fermented and naturally triggers the stomach to produce acid for food breakdown.

A little goes a long way but even just a teaspoon at the start of a meal can offer relief. (Some people experience an increase in burning sensation with apple cider vinegar, so ease into this if you’d like to try it.)

Nutrients for GERD (and Thyroid Support!)


The mineral magnesium plays a number of roles in the body but a major one is the contraction and the release of muscles.

Then it may come as no surprise that a magnesium deficiency is linked to a disorder that comes from a loose sphincter.

There are many antacid products that include magnesium. But a better source would be straight-up magnesium supplement, getting closer to the source of the problem.

A simple supplementation of 200 to 400 mg twice per day should do the trick.

Magnesium is a powerhouse for Hashimoto’s too so this is a real two-fer.

Probiotics to Support your Thyroid and Gut

You’ve learned about the strong connection between the thyroid and the gut. One of the best ways to help support that “friendship” is with probiotics.

Traditionally, most cultures have included fermented foods in their diets. But American society use much fermented foods and as we’ve phased them out, out gut flora has paid the price.

Naturally fermented foods like kimchi, sauerkraut (not all are fermented, it has to be the refrigerated kind), natto, kefir and kombucha are a great way to get your probiotics.

But probiotic supplements can actually give you better numbers and variety.

Look for supplements with CFUs (colony forming units) in the billions and with multiple strains.

Vitamin B12

Another nutrient deficiency associated with GERD is the vitamin B12. Studies have found the people who take PPIs long term are more prone to B12 deficiency.

B12 is also necessary for the conversion of T4 to T3, so it’s a strong thyroid supporter in cases on Hashimoto’s.

While we get some of our B12 from our food, another portion of our B12 is actually made in our gut.

But this can only happen when the gut is in balance with good bacteria.

Other Supplement and Food Options to Remedy Acid Reflux

A quick online search will give you a hearty list of “remedies” for acid reflux.

But the truth of the matter is that most of these will just give you some temporary relief. And of course you may want some relief but you also want to get to the root of the problem.

For relief from acid reflux, you can try:

  • Digestive enzymes before each meal
  • Ginger (fresh or in capsule form)
  • Licorice root supplements
  • Aloe vera juice, gel or capsules
  • DGL (deglycyrrhizinated licorice) lozenges

But if the problem is low stomach acid, consider what would help build it back up.

As I mentioned, apple cider vinegar naturally stimulates the body to make stomach acid (but go slow!) Other options include:

  • Hydrochloride (HCl), which is the main component of stomach acid, with the enzyme pepsin before a meal
  • Betaine /TMG (not to be confused with Betaine HCL) has an overall parasympathetic effect and may help where chronic stress activates the opening of the LES.
  • Digestive bitters or lemon juice in water, which act the same way apple cider vinegar does too stimulate stomach acid

The problem with going the medication route is that the pharmaceutical industry still treats GERD as a high-stomach acid issue.

Lifestyle Changes for Digestion to Relieve Acid Reflux

In addition to what foods and supplements you do and don’t eat and take, there are a number of lifestyle choices that you can make that can have a huge impact on chronic reflux or GERD.

Stopping smoking and losing weight in a healthy way are probably two of the biggest (and hardest) changes you can make to support your digestion to prevent acid reflux.

Overeating or eating beyond where you’re full pushes food up toward that LES, exacerbating GERD. Also, eating too close to when you sleep has a similar effect. Eating at least 2-3 hours before bedtime can help.

Even something as simple as sitting up straight while you eat might seem small but can impact digestion.

A little less simple is not eating when you’re stressed. This may not always be an option of course. But cortisol, a stress hormone, decreases the production of stomach acid.

You might even close your eyes and take a few calming breaths before you eat to help ease you out of fight-or-flight mode.

Gut Health for Your Thyroid, Thyroid Health for Your Gut

If you’re like me, some health issues loom larger, while others get put on the back burner. If you’ve been dealing with Hashimoto’s, you may have felt like your acid reflux experiences can wait to be worked on.

But we know that the long-term effects of GERD can be just as serious.

The good news that I hope has been your takeaway, is that when you work on your thyroid health, your gut health can improve. And vice versa.

Even small changes in your diet and lifestyle will help find you relief from your GERD and therefore make some adjustments to your thyroid as well.

To learn more about how to improve your Hashimoto’s hypothyroidism, check out my Nourished and Renewed With Hashimoto’s program.

Need more specialized and personalized care? MyHappy & Healthy with Hashimoto's Program is just the right fit!

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The information on this website is for educational purposes only and should not be considered medical advice. This information is provided to help you make informed decisions about your health. It is not meant to replace the advice of your primary physician.

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