Many moons ago, I was chronically exhausted and needed to sleep for 11 to 12 hours to feel human. Things didn’t get much better, despite starting thyroid medications in 2010, and even going gluten- and dairy-free in 2011. The medication did reduce my cold intolerance, need for sleep by about one hour, and anxiety. Furthermore, eliminating dairy and gluten helped to stop my acid reflux, irritable bowel syndrome, and joint pain, as well as reduced my thyroid antibodies… but my symptoms of fatigue and brain fog persisted.
When I first became chronically exhausted, I would sleep as long as possible. This was much easier as a college student. Unfortunately, it led to having less time to study for my exams, but I soon learned to compensate. I would sleep all day, then stay up all night to study. After taking my exams at 7:30 am, I would then come home and sleep more.
Other times, when I had to wake up with fewer than 10 hours of sleep, I would often be struck with diarrhea. I remember saying to my mom, “It’s like I need to sleep so that my body can process everything I ate, and when I wake up too early, it’s still not processed.”
I started taking one new supplement on Friday, February 10th, 2012 — one capsule with each meal. I was surprised to wake up the following morning at 8 am, without an alarm. I had been dragging myself out of bed after 10 am most mornings that I did not have to work. Strangely, I continued to feel energetic all day. I even stayed awake when my usually much more energetic husband took a nap.
Within two short days, things became easier, and all of a sudden, I felt that I had a surplus of time… I felt more at ease going to bed, and even had time to meditate — something that I had been telling myself to do for months. As the week went on, I felt myself having more and more energy, and actually became more and more talkative. Additionally, the mental fog had completely lifted, and I could come up with all sorts of clever words quickly. My co-workers commented on my good mood at work. My husband noticed that my sense of humor had improved as well.
This supplement was betaine with pepsin — an enzyme used to support protein digestion. I want to share a little more about this one supplement that was my first “AHA” moment for getting my health (and life) back.
In this article, you’ll discover:
- How common low stomach acid is in those with Hashimoto’s
- How betaine with pepsin can help Hashimoto’s and pain
- Who should not take betaine with pepsin
- Recommended betaine with pepsin supplements and proper dosing
- Additional ways to support low stomach acid
Low Stomach Acid and Hashimoto’s
If you’ve been following me for a while, you’ll likely have heard me talking about betaine with pepsin — one of the most helpful supplements I came across during my health journey. I often tell the story about how this supplement changed my life.
You may have been told that you have too much stomach acid, and that you need to go on medication to help reduce the acid your stomach is producing… And chances are that, if you’re like me, you’ve taken the advice of mainstream doctors and websites, but still don’t feel well or “human.”
What if I told you that it may actually be the opposite — that you may not be producing enough stomach acid?
Studies have found that people with Hashimoto’s and hypothyroidism, often have hypochlorhydria (low stomach acid) or achlorhydria (lack of stomach acid).  When we have low stomach acid, we are at greater risk for many undesirable health consequences:
- Contracting parasites from our food – Stomach acid helps us sterilize our food, killing off potential infecting pathogens. 
- Food sensitivities – Proteins that are not properly broken down, are more likely to induce an antigenic response from our immune system, leading to food sensitivities (especially to gluten and dairy). 
- Small intestinal bacterial overgrowth (SIBO) – Without stomach acid, which keeps them at bay, bacteria in the small intestine may grow and thrive on poorly digested proteins. In one small study, 54 percent of people with hypothyroidism were found to have SIBO. 
- Nutrient depletions – Especially in calcium, iron/ferritin, and B12. 
If prolonged, low stomach acid can lead to hypergastrinemia (excess secretion of gastrin, another digestive enzyme, as a compensatory mechanism due to low stomach acid), which can lead to tumors/cancerous growth in the gastrointestinal tract.
Symptoms of Achlorhydria or Hypochlorhydria
There aren’t too many tell-tale signs of low stomach acid, other than perhaps feeling full and tired after meals, as well as experiencing acid reflux-like symptoms. Nonetheless, low stomach acid is very common in Hashimoto’s.
Signs and symptoms that would lead me to believe that a person with Hashimoto’s has low stomach acid include:
- Acid reflux (this condition, which is conventionally treated with acid suppressants, can actually be caused by low stomach acid)
- Low B12
- Low ferritin or iron levels
- Fatigue despite thyroid medications
Another interesting symptom that could point to low stomach acid is post-nasal drip. This is because when the contents of the stomach travel up to the esophagus (as it does in acid reflux), this can lead to irritation of the nasal passages and the sinuses, which then may react by producing mucus that drips into the throat. 
What is Betaine HCl and Pepsin?
Betaine HCl and pepsin (also known as betaine hydrochloride and pepsin, or simply betaine and pepsin) are naturally occurring components of gastric juice that make nutrients and amino acids from our protein-containing foods more bioavailable, by breaking down protein bonds. They are especially important for the proper absorption of protein, calcium, B12, and iron.
Betaine, also known as trimethylglycine, is a naturally occurring amino acid derivative that is isolated from beets, and the acidic HCl version of it promotes acidity in the gastric opening. Betaine HCl used to be available as an over-the-counter (OTC) drug, marketed as a stomach acidifier and digestive aid.
It was later removed from OTC use in 1993 due to insufficient evidence of it working, and was banished to being a dietary supplement by the FDA. Please note that this difference means dietary supplement companies cannot make claims of the effectiveness of their products, while drug companies can make specific claims. However, studies done in 2013 did indeed find that betaine HCl can re-acidify gastric pH. 
Pepsin is a naturally occurring digestive enzyme that breaks apart proteins into smaller pieces so they can be properly absorbed by the small intestine. In supplements, pepsin is usually derived from porcine sources.
How Betaine with Pepsin Can Help with Hashimoto’s
In my 2015 survey of 2232 people with Hashimoto’s, out of 627 people who took betaine HCl and pepsin…
- 59 percent said that it made them feel better
- 33 percent said that it made them feel worse
- 7 percent saw no difference in symptoms
The improvement rates lead me to believe that 50-70 percent of people with Hashimoto’s are likely deficient in stomach acid. Those that felt worse were likely not deficient, as taking the supplement can make a person with adequate stomach acid feel worse for a short time (burning in the throat and stomach upset may occur). Those that did not see any improvement may not have been dosed adequately, as betaine with pepsin dosages needs to be individualized.
The biggest improvements seen after taking this supplement were improved energy levels (58 percent), reduced pain (40 percent), and improved mood (35 percent). One-fourth of the people who took betaine with pepsin felt that this supplement also helped them with losing weight.
Betaine HCl and pepsin can make a tremendous difference in a person’s symptoms because, once we begin to digest our proteins correctly, a few great things can happen:
- The body may not need to expend as much energy on digestion, and since digestion is one of our body’s biggest energy expenditures, we often begin to have a surplus of energy.
- The amino acids found in proteins become bioavailable, helping with the creation of neurotransmitters and fuel for our bodies.
- We will be less likely to react to our foods, as the food particles will get broken down into individual amino acids before they move further down into our gut.
- We will feel lighter after we eat, and will not have cravings for food when full.
Pain and Hashimoto’s
When we assist our digestion with the use of betaine with pepsin, it is possible to reduce pain.
As I mentioned above, 40 percent of people with Hashimoto’s reported a reduction in pain with the use of betaine with pepsin.
Why does betaine with pepsin reduce pain?
At first, this question caught me a bit off guard, but the more I thought about the mechanism of action, the more it made perfect sense. Betaine and pepsin break down protein bonds in food, thereby aiding digestion, reducing intestinal inflammation, and even leading to reduced systemic inflammation and less pain for many people.
Betaine can also help break down homocysteine, which has been associated with inflammation and increased risk of cardiovascular conditions, especially for those with the MTHFR gene mutation (more on the MTHFR gene mutation in the sections below).
Furthermore, betaine can increase the amount of SAMe, a naturally occurring substance with mood-boosting and pain-relieving properties, within the body.
Who Should Avoid Betaine with Pepsin?
Using this supplement in excess can lead to stomach irritation, and I always recommend a slow dose titration to determine your optimal dose.
That said, some people should NOT take betaine with pepsin. This supplement should not be used by those with a history of peptic ulcers* or gastritis**, those with an active H. pylori infection, or those with an overproduction of acid. Discuss with your primary care practitioner before taking if you are pregnant or breastfeeding.
(*Signs and symptoms of an ulcer include a dull pain in the stomach, weight loss, nausea/vomiting, acid reflux, bloating, and burping. Pain improves when you eat, drink, or take antacids.
**Signs and symptoms of gastritis include a gnawing/burning feeling in your upper abdomen, nausea/vomiting, and fullness after eating. Symptoms can improve or get worse after eating.)
Do not take betaine with pepsin if taking blood thinners, non-steroidal anti-inflammatory drugs (NSAIDs), steroids, or other medications that may increase one’s likelihood of developing an ulcer. I also recommend avoiding this supplement if you are taking proton pump inhibitors or other acid-suppressing medications, as these will negate the effect of the supplement.
Additionally, while having hypothyroidism or Hashimoto’s in itself can cause low stomach acid, as can aging and genetics, there are other root causes of low stomach acid that need to be considered.
Addressing these root causes should always be done in conjunction with betaine HCl and pepsin supplementation:
- H. pylori infections, which can trigger Hashimoto’s.
- B12 deficiency, which may be associated with a vegan diet or with anti-parietal cell antibodies (proteins that are produced by our immune system and mistakenly target specific cells within the stomach lining).
- Adrenal dysfunction, which can deplete nutrients required for stomach acid production.
- The MTHFR mutation, which is associated with a buildup of homocysteine due to impaired methylation. There are two main pathways of breaking down homocysteine. One of them involves the use of trimethylglycine (betaine), and this gene mutation could theoretically make someone trimethylglycine deficient.
- Other nutrient deficiencies, especially thiamine.
Proper Dosing of Betaine with Pepsin
Betaine HCl and pepsin should be taken with a protein-rich meal, starting with one capsule per meal. The dose should be increased by one more capsule at each meal, until symptoms of too much acid are felt (burping, burning, warming in the stomach region, etc.). At that point, you will know that your dose is one capsule less than what resulted in symptoms.
Drinking a mixture of one teaspoon of baking soda in a glass of water, can reduce these temporary symptoms.
- Meal No. 1: Took one capsule, didn’t feel symptoms
- Meal No. 2: Took two capsules, didn’t feel symptoms
- Meal No. 3: Took three capsules, didn’t feel symptoms
- Meal No. 4: Took four capsules, felt symptoms
- Target dose: Three capsules (one capsule less than what resulted in symptoms)
I recommend Rootcology Betaine with Pepsin, which provides 750 mg of betaine hydrochloride, along with pepsin, and is free of fillers and common reactive ingredients like gluten, dairy, soy, and pesticides.
I also like the Betaine HCL supplement from Pure Encapsulations, which contains vitamin C derived from non-GMO corn dextrose, in addition to betaine and pepsin. The dextrose, a corn sugar, is consumed in the creation of the vitamin C and does not contain corn proteins, which are the reactive component of corn for most people with Hashimoto’s who are corn-sensitive. The supplement itself is hypoallergenic.
Alternate Ways to Support Stomach Acid
Others have found that diluted apple cider vinegar or lemon juice can support digestion in some cases of low stomach acid. For apple cider vinegar, I recommend one teaspoon of apple cider vinegar in one glass of cold water. For lemon juice, I recommend squeezing the juice of one lemon into a cup of hot water. Please note that these substances should also not be used with an ulcer or gastritis.
If you want to take betaine and pepsin to help break down homocysteine due to having the MTHFR gene mutation, please note that beets are also a rich source of betaine, and their betaine content can break down homocysteine. (Individuals with the MTHFR gene mutation have trouble processing the amino acid homocysteine, elevated levels of which have been associated with heart disease, difficult pregnancies, birth defects, and possibly an impaired ability to detoxify.) One to two servings per week would be recommended — and since they are high in sugar, you will want to pair them with a healthy fat or protein source.
The connection between low stomach acid and Hashimoto’s was a huge “AHA” moment for me, and led me to write my first book. I had always loved writing and dreamed of writing a book that would help others, but I thought becoming an author would be impossible — especially while working at a full-time job and with my 12-hour sleep demands!
Once I started to take betaine with pepsin, I had a breakthrough. I discovered that I had low stomach acid… and it was truly affecting my thoughts, the pain I was experiencing, my extreme fatigue, and my every move. When those symptoms resolved and my energy started to skyrocket, I was finally able to follow my dream and write a book to help others with Hashimoto’s.
I hope this article sheds some light and brings hope to you if you are suffering from any of the above symptoms — pain, fatigue, gastric infections, and acid reflux, to name a few. Finding your proper dose of betaine with pepsin may bring you relief so that you, too, can follow your dreams that may have been held back due to low stomach acid.
As always, please discuss the use of supplements with your personal doctor or pharmacist. This article is for informational purposes only, and I am not able to advise on whether this or any other supplement would be appropriate for you and your specific health needs, without a comprehensive health assessment.
I hope this information helps you on your journey!
I’d love to hear from you! Have you been having trouble with symptoms of acid reflux? Have you tried betaine with pepsin and seen improvements with supplementation?
P.S. I love interacting with my readers on social media, and I encourage you to join my Facebook, Instagram, TikTok, and Pinterest community pages to stay on top of thyroid health updates and meet others who are following similar health journeys. For recipes, a FREE Thyroid Diet start guide, notifications about upcoming events, and the Nutrient Depletions and Digestion chapter from my first book for free, be sure to sign up for my email list!
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Note: Originally published in October 2015, this article has been revised and updated for accuracy and thoroughness.