Informational Posts

Acid Reflux, Low Stomach Acid and Hypothyroidism

Acid Reflux, Low Stomach Acid and Hypothyroidism
Originally published on 27th May 2016
Last updated on 1st September 2023

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 stomach acid issues, namely low stomach acid, which leads to GORD, GERD, acid reflux, heartburn, indigestion, difficulty swallowing, chest pain/discomfort, coughing and even hoarseness.

With symptoms of acid reflux, you may also feel very full, sick, bloated or tired after eating.

Acid Reflux and Low Thyroid Levels 

Most common for those on T4-only medications such as Levothyroxine or Synthroid, non-optimally treated hypothyroidism or Hashimoto’s can be linked to stomach acid problems.

It seems that hypothyroidism lowers levels of stomach acid and this could be due to a lowering of parietel cells, reducing their ability to produce gastric acid (hypochlorhydria).

Because of this, the absorption of nutrients is reduced (such as vitamin D, b12, ), which can lead on to low or deficient levels of certain too.

Acid reflux issues may also be caused by poor gut health, which often goes hand in hand with thyroid disease.

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 once taking Omeprazole for daily acid reflux. This was back at the beginning of my diagnosis, when I was on Levothyroxine only for hypothyroidism. However, I never responded well to this treatment and many symptoms were ongoing or new ones appearing on this medication.

Once I switched to natural desiccated thyroid, and corrected (optimised) all my thyroid hormone levels, acid reflux and all other issues disappeared, and I no longer needed the Omeprazole.

It’s the case for a lot of thyroid patients; doctors keep handing out more and more medications, refusing to acknowledge that it’s all linked, and that by giving medications for acid reflux, it’s not treating the cause or at least a big contributor – low thyroid levels. You may also find that getting your thyroid levels optimised could well correct or improve a whole host of and symptoms you have, too.


Skipping meals, ignoring hunger, eating too much sugar, fatty meals or drinking or can worsen acid reflux or trigger it directly. So keep these in mind and trial whether any are contributing to yours.

Also, any disordered eating behaviours (such as skipping meals, ignoring hunger, eating a really low-calorie diet etc.) can also contribute to stomach issues. Some experience more reflux when they are not eating enough, or often enough (smaller snacks may work better than fewer, large meals). 

We can trial less sugar, , dairy, reducing and , and figuring out if any food sensitivities are causing reflux with an elimination diet.

Learning how to and introducing gut-loving, helpful foods such as chia seeds, coconut oil, turmeric, cinnamon, flaxseed, hemp oil, oregano and garlic, all to support your gut health may also help.

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. 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.

Autoimmune Atrophic Gastritis

This condition occurs when your immune system attacks the cells of your stomach lining cells. It may also be referred to as autoimmune gastritis (AIG) or autoimmune metaplastic atrophic gastritis (AMAG).

When you already have one autoimmune disease (such as Hashimoto’s, which most people with hypothyroidism have), you are a lot more likely to develop another, including Autoimmune Atrophic Gastritis.

Tests used to check for this condition can include an Anti Parietal Cell Antibodies Test, Serum Gastrin Test, as well as tests for B12 and iron stores which can be very low with this condition.

This condition is quite rare, but people who those with thyroid disease are more likely to have it. You are also more at risk if you’re African-American or of northern European descent. AIG can increase your risk of stomach cancer.

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.

About Author

Rachel Hill is the highly ranked and multi-award winning thyroid patient advocate, writer, speaker and author behind The Invisible Hypothyroidism. Her thyroid advocacy work includes writing articles, authoring books, producing her Thyroid Family email newsletters and speaking on podcasts and at events about the many aspects thyroid disease affects and how to overcome these. She is well-recognised as a crucial and influential contributor to the thyroid community and has a large social media presence. Her bestselling books include "Be Your Own Thyroid Advocate" and "You, Me and Hypothyroidism".


  • Lena
    February 14, 2023 at 4:58 am

    Hi Rachel, your article totally describes what I have been going through over the last 7 years. Ever since I started taking Levothyroxine I have major acid reflux issues. My doctor refuses to acknowledge my issues are linked and no other help is offered to me. Did you stop taking Levothyroxine completely? What is the medicine that you replaced it with? Any help is greatly appreciated. Thank you

    • Rachel Hill
      February 19, 2023 at 2:28 pm

      Hi Lena – the reflux resolved for me when I switched from Levo to Armour, plus went gluten-free.

      • Daisy
        April 6, 2023 at 6:15 pm

        Hi Rachel ,
        how did you get the Armour as I take t 3 and T 4 and have awful wheeze after food .never had it prior to taken meds , i have no thryoid .
        I can see its private did your endocrinologist help you get the pricription ?
        Thanks Daisy.

  • Ponto do Rateio
    January 14, 2023 at 5:31 pm

    I’m so happy to read this.

  • B Doyle
    May 20, 2021 at 3:12 pm

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

  • Romaine Cohen
    September 14, 2018 at 8:41 am

    Saved as a favorite, I really like your blog!

  • Linda Fee
    June 17, 2018 at 5:03 pm

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


Leave a Reply