Acid Reflux, Low Stomach Acid and Hypothyroidism

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Stomach acid is needed in the body to break down food and get rid of bad bacteria.

It is made as and when you eat, but many hypothyroid patients have low stomach acid, which leads to GORD, GERD, acid reflux, heartburn, indigestion, acid regurgitation, difficulty swallowing, chest pain/discomfort, cough and even hoarseness. You may even feel very full and tired after eating.

As you get older, your levels of stomach acid can decrease, but many hypothyroid patients are surprised to learn that their acid reflux can be related to a poorly treated underactive thyroid, hypothyroidism or Hashimoto’s. In fact, Studies have found that people with hypothyroidism (and especially Hashimoto’s) often have low stomach acid.

Acid Reflux and Low Thyroid Levels 

Most common for those on T4-only medication like Levothyroxine or Synthroid, a non-optimally treated underactive thyroid, hypothyroidism and/or Hashimoto’s can be linked to these low stomach acid problems.

It seems that hypothyroidism can lower levels of stomach acid and this could be due to a lowering of parietel cells, lowering their ability to produce gastric acid (hypochlorhydria). Because of this, the absorption of important nutrients is reduced (such as vitamin D, b12, iron etc.), which can lead on to low or deficient levels of certain vitamins. Lowered levels of vitamins and minerals is common with hypothyroid patients and especially those with Hashimoto’s due to leaky gut for example. 

Prescription Medications 

Low levels of stomach acid can lead to your doctor diagnosing you with gastritis, which is basically inflammation of the lining of the stomach.

Like me, doctors put most thyroid patients with these problems on PPI medications like Omeprazole, which are acid suppressors, when we may already have low levels of stomach acid. These medications therefore mask the symptoms and problem, which just makes things worse, because the actual issue of why you have low stomach acid isn’t being addressed.

Optimal Thyroid Levels 

The main thing you can do is to make sure your thyroid condition is optimally medicated. Whether you’re on T4-only meds like Levothyroxine or Synthroid, a T3 and T4 combo or NDT, you want to aim for optimal levels.

Low thyroid levels can cause low stomach acid.

I was on Omeprazole for my daily acid reflux, but once I started NDT and corrected my thyroid levels, my acid reflux problems greatly improved. It’s the case for a lot of thyroid patients; doctors just keep handing out more and more medications, refusing to acknowledge that it’s all linked, and that by giving meds for acid reflux, it’s not treating the cause or at least a big contributor – low thyroid levels. You’ll find that getting your thyroid levels right could well correct or improve a whole host of other health conditions you have, too.


I have also noticed that skipping meals, ignoring hunger, eating too much sugar, high fat or drinking alcohol significantly worsens my acid reflux or gives me acid reflux directly. None of these are good habits!

Apple Cider Vinegar 

Apple cider vinegar is said to help raise low stomach acid also, and can help with digestion.

Adding a little to a morning drink is reported to be effective. I’ve read about a lot of thyroid patients using this brand – Braggs Organic Apple Cider Vinegar, 473ml.

My functional medicine practitioner has me take two tablespoons of apple cider vinegar in warm water with each meal (though using a straw as it can be damaging to teeth), and it does help me digest food and have less issues with acid reflux or heartburn.


Checking for iodine deficiency and restoring any low levels may also improve stomach acid production as well. It’s not wise to guess if you have low iodine levels, as supplementing it when you don’t need it, can make your hypothyroid situation worse and it can be dangerous, especially for those with Hashimoto’s.

Gut Health

Some people also find that adding a probiotic to their health regimen helps, as it can help to balance out the good and bad bacteria. Anything that improves or aids gut health and function can certainly help. More info on that here.

Along the same kind of lines, a digestive enzyme or Betaine HCl and Pepsin can also help, as they aid the digestion process. Going gluten-free can also be a good step for many thyroid patients.

But it’s very important to address your gut completely if you have digestion issues or complaints. This includes your diet, Candida, leaky gut, food sensitivities and infections. More information can be read in this article. A UK test for Candida can be found here and a US test here.

Hope For No Reflux 

As you correct your low stomach acid, the ability to absorb nutrients and minerals should also improve, as well as relief of acid reflux, heartburn etc. but when coming off medication for acid reflux, heartburn, GERD etc. make sure to do it with a doctor’s guidance, and wean off of them slowly to avoid nasty side effects.

Have you experienced reflux or other indigestion with your thyroid condition?

You can click on the hyperlinks in the above post to learn more and see references to information given.

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5 thoughts on “Acid Reflux, Low Stomach Acid and Hypothyroidism

  1. Your writing style is so unique compared to many other thyroid people. Thank you for publishing when you have the opportunity.

  2. Its like you read my mind! You appear to know so much about
    this, like you wrote a book in it or something.

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