ULTIMATE Step By Step HCl Guide for Reflux Sufferers

If you are new to this site, you should first read my How I Cured My Silent Reflux article as it explains the underlying root causes of acid reflux, its corresponding treatments, and provides the necessary context to follow some of the concepts in this episode.

Episode Transcript

(Note this is not a word-for-word transcription - it's loosely paraphrased. Alternatively, feel free to watch on YouTube).

Welcome to episode #5 of The Reflux Cycle show. My name is Don, also known as The Acid Reflux Guy. Today’s episode is all about Betaine Hydrochloride. I will provide an overview and then get into the questions you submitted over the past week.

Let me know if I’ve missed anything and if there are enough outstanding questions I’ll do an encore episode.

Before we dive in, I do need to remind you that the information included in this show is for educational purposes only and is not intended to be a substitute for medical treatment by a healthcare professional. Because of unique individual needs, listeners should consult their physician to determine the appropriateness of the information for their situation.

To Start With, What is Betaine Hydrochloride?

Betaine hydrochloride is a nutritional amino acid extracted from food sources like grains, beets, spinach, beef, shrimp, and whole wheat foods.

It was originally found in beets and that’s where the name betaine comes from. It is called Hydrochloride because Betaine Hydrochloride is the hydrochloride salt of betaine.

This acidic version of betaine works in the same way as the body’s own hydrochloric acid (HCl), and can serve as a supplemental source in your stomach to lower the pH and assist with digestion. This, as stomach acid should normally be in the low 1.5 – 3 pH range.

“In the stomach, betaine hydrochloride separates into betaine and hydrochloric acid. As you might expect, the hydrochloric acid is supplemental to the body’s own stomach acid.

Betaine hydrochloride is recommended by some doctors as a supplemental source of hydrochloric acid for people who have a deficiency of stomach acid production, known as (hypochlorhydria) or low stomach acid.

When low stomach acid is present, the body is unable to absorb vitamins and minerals, break down proteins, and kill bacteria and viruses that enter the stomach orally.

Many people intuitively, albeit incorrectly, believe that they have high stomach acid. This idea is even sometimes reinforced by well intentioned, yet misinformed medical providers.

There are a few diagnostics that can determine empirically if you have low stomach acid including the Heidelberg test and a Serum Gastrin Test. Unfortunately, however use both diagnostics are rare.

Not every reflux sufferer has low stomach acid. But In episode 002 , I covered six reasons you may have low stomach acid. However, there are others such as certain vitamin deficiencies (we’ll cover later), aging, and reduction of short chain fatty acids driven by microbial imbalance of the gut.

Quite often, insufficient acid production is paired with insufficient pepsin production, causing the body to struggle to digest food.

This is why you may want to ensure your variety of betaine HCl contains pepsins as these help to break down proteins into smaller, more easily absorbed substances.

How does it work – case study

Looking at a case study published in the US National Library of Medicine, we learn the onset of betaine HCl is rapid, quickly prompting temporary re-acidification and lasting about an hour (±30) minutes.

The study looked at people who were pharmacologically achlorhydric, which means their acid reflux medications where doing what they are designed to do and rendering their resting gastric pH in the 5-7 pH range, which is slightly to non acidic.

In the study, betaine safely reduced gastric pH from above pH 5 to pH 1 for about an hour.

Second case study

I’ll link a second case study in the show notes. It follows a patient with irritable bowel syndrome and how they effectively used betaine HCl to re-acidify and address reflux medication induced hypochlorhydria or “low stomach acid.”

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So, who Shouldn’t Take Betaine HCl?


People that have certain allergies. For instance, the brand that I used doesn’t contain yeast, eggs, gluten, soy, wheat, sugar, starch, salt, preservatives, fragrance, artificial colors, or artificial flavors.

Individuals with inflammatory conditions such as ulcers, gastritis, or esophagitis or that take medications that increase risk factors for these conditions.

The safety and efficacy of betaine HCl supplements have not been clinically evaluated in children or pregnant or breastfeeding women.

HCl can irritate sensitive tissue and can be corrosive to teeth; therefore, capsules should NOT be emptied into food or dissolved in beverages. Similar consideration for those with trouble swallowing as pills can become lodged in the soft tissues of the throat.

It s important that HCl is taken with a meal of sufficient size (500 calories or more) containing adequate protein. Betaine HCl should not be taken on an empty stomach unless it is followed immediately by consuming a meal. Even so, I find that taking it a few minutes into the meal is best for reasons we’ll cover shortly.

Side Effects

Potential side effects include diarrhea, nausea, body odor, or reflux sensations such as stomach discomfort.

Betaine Hydrochloride doesn’t increase stomach acid to a level beyond what is normal in the stomach. As such, if there is any burning sensation it may be an indication of compromised stomach mucosal lining.

Warning labels on the supplement indicate that if a burning sensation is experienced you should discontinue use, or use less frequently. This, as that continued use could further degrade the lining of your stomach.

History of Betaine

Betaine has an interesting history. It used to be included in OTC medications to help with digestion. However, in 1988 they added section 310.540 which stipulates they cannot be classified a drug

“Because of the lack of adequate data to establish the effectiveness of these or any other ingredients for use in treating achlorhydria and hypochlorhydria, and because such conditions are asymptomatic, any OTC drug product containing ingredients offered for use as a stomach acidifier cannot be considered generally recognized as safe and effective.”

I want you to hold on to the fact that the FDA has declared achlorhydria (low stomach acid) and hypochlorhydria (low stomach acid) as asymptomatic, meaning there re no symptoms with these conditions. We’ll come back to this in a second.

Nonetheless, given this FDA regulation, betaine supplements may now only be labeled as dietary supplements and are unregulated by the FDA.

According to WebMD,

“Promoters still claim that some health conditions are due to inadequate stomach acid, but this claim has not been proven. Even if it were true, betaine hydrochloride wouldn’t help. It only delivers hydrochloric acid but does not itself alter stomach acidity.”

However, this contradicts my experience, recommendations from holistic, naturopathic, functional medical providers, AND even the user reviews posted on WebMD, which are overwhelmingly positive! Link in the show notes if you want to check them out for yourself!

What are some of the Benefits of Betaine HCl

  • This supplement supports digestion,
  • helps to support healthy gut function, and safely restore normal gastric acidity
  • More importantly, acidity along with increased intra-abdominal pressure, are the triggers your body needs to signal your lower esophageal sphincter to close and prevent the backflow of stomach contents into the throat
  • Additionally, acidity is required to signal the pyloric sphincter to efficiently and effectively release stomach contents into the small intestines.
  • Lastly, achieving optimal stomach acidity helps your body to rebalance your microbiome as beneficial microbes thrive in the naturally high acidity found in the gut; non-beneficial microbes are allowed to flourish in the presence of insufficient acidity.

These factors are often key to enable you to stop taking your prescription or over-the-counter reflux medications and antacids. This, as acid reflux medications compromise your stomach’s acidity which is many times a contributing factor to the issues I just mentioned. Let me read a quote to you from a medical journal published in the National Institutes of Health.

“Generally, a fasting gastric pH less than 3.0 is considered “normal,” while values above 3.0 are deemed to be gradually more hypochlorhydric. True achlorhydria results in a gastric pH above 7, which is characterized by very limited acid production even when stimulated by gastrin or histamine. Subjects taking proton-pump inhibitors will generally have a fasting gastric pH between 5-7.”

The article continues:

“Inadequate levels of stomach acid (regardless of the root cause) can result in many nutritional and digestive issues. For instance, a reduction in gastric acid secretion prevents adequate denaturing of folded proteins resulting in poor protein digestion and increased food allergenicity. Activation of pepsin (from pepsinogen) is greatest at a pH of 2 or less and its protease activity is optimal at a pH of 1.8 to 2.3. A low-acid environment is linked to reduced absorption of key micronutrients such as calcium, iron, folic acid, vitamin B6 and vitamin B12. Also, since gastric acid helps to eliminate harmful ingested microorganisms and hinders bacterial overgrowth in the stomach and small bowel; low stomach acid can increase the risk for small intestinal bacterial overgrowth (SIBO) and specific microbial overgrowth from organisms like Clostridium difficile. While most of these consequences of low stomach acid are undisputed, there is much less agreement on the prevalence of this condition in the general population, how to test for such a condition and, especially, whether there is an appropriate therapy for low stomach acid..

How do you take Betaine Hydrochloride?


People often ask me, well I don’t feel any discomfort with HCl so how do I know if I’m taking the right dose? Well, I’ll walk you through the eight steps, using a guide published in the National Institutes of Health which sheds some light on what you can additionally be looking for. The title of the article is “Meal-Time Supplementation with Betaine HCl for Functional Hypochlorhydria: What is the Evidence?” For a link to guide on how best to take Betaine HCl see the show notes.

I want to add to this, some of my leanings while taking Betaine

  1. It is sub-optimal to take HCl with reflux medications. This study shows that taking it while on PPIs increases the time for re-acidification three fold.
  2. It is best not to take betaine on an empty stomach or before meals. Instead, take in the middle of meals. The prior article further explains that taking it 10 minutes into meals reduces the chances of delayed re-acidification. Additionally, my own experience and that from talking to people that contact me, is taking it just before meals can be uncomfortable and provide a false negative.
  3. A common pitfall is people find or decided to use HCl with no pepsins, thinking pepsins are bad. As we have covered pepsins are a key part of digestion and are often in low supply or are not activated when stomach acidity is compromised
  4. Taking a combined HCl and digestive enzymes or other supplements, doesn’t allow for HCl dose to be varied as necessary. Also, betaine as an added benefit is often below the recommended dosage range
  5. Some people never feel the discomfort and keep upping the dose, hoping that they will. Taking too much can of course, be unsafe
  6. Same dose doesn’t work for every meal, it definitely needs to be varied according to meal complexity.

How long can someone stay on betaine HCl?

This is a good question for your doctor. Aside form the warnings mentioned prior, I have not been able to locate any reasons why an individual could not take HCl long-term. However, the goal is to use it in the short term as a tool to help accelerate healing an ultimately to get off of this and all supplements.

Can you heal without or with less betaine?

This is not something I have personal experience with, however I do believe it is possible. If I were faced with not being able to take HCl as a part of my healing regime, I would focus on anti-inflammatory actions that I could take such as high fiber daily, avoiding sugar / fatty foods, taking a probiotic, and avoiding triggers. After doing that for a while I would begin weaning my dose of reflux medication. This will, of course be a much slower process, but based on my understanding of the underlying issues I expect it could also be successful.

What was your experience with HCl?

How did you feel compared to PPI?

For me, the effects of the dietary changes and three supplements that I took, including the HCl, were immediate and profound.

I took them one night for dinner and when I woke up the next morning I felt better than I had in 15 years. For the first time, I didn’t wake up with a mouth full of stomach contents. I felt that my throat was closed. In fact, the effects were so profound that I called in a vacation day and started theacidrefluxguy.com. After suffering so long with no help, I just knew that I had to get this information out to more people.

I suspect my results were so immediate because of my unique microbial imbalance. The HCl likely helped to kill off bacteria that were disrupting the interactions between my microbiome and my enteric nervous system and as a result digestive function such as opening and closing of my lower esophageal sphincter was improved. That coupled with low acidity did not allow the proper signals to deliver sufficient closing pressure.

Not everyone has such an immediate experience though. For some, re-balancing and rebuilding key microbial species takes time. Even though I had such a profound experience, I still spent the next eight weeks rebuilding my gut. There were ups and downs as I experimented with what worked and what didn’t, especially with the HCl.

At the time, I didn’t have the guide that I shared wit you today. Much of what I did, including the dietary changes and supplements, I had to piece together from many sources.

How long did it take to find your personal dose?

Finding your personal dose is a continual process as you will be adjusting your dose as necessary from the first time you take it, until you are down to your last pill. As the article I shared covered, when your experience discomfort it is a cue to reduce the dose by one capsule.

The dose will also vary according to the size and complexity of individual meals. For example, I often took 2-3 with dinner, 4-5 for very high protein meals, and 1-2 for lunch and 0-1 for breakfast. Over time, by paying close attention to your body, you will gain a sense for the right dose.

Many times I didn’t feel any discomfort with the HCl so I didn’t always have that as a guide. As such, I periodically experimented with reducing my dose. I saw a noticeable difference in my symptoms for when I took it and when I didn’t. For instance, my nose would run more when I didn’t take enough. I would experience mild regurgitation or clearing of my throat off and on and depending on what I ate.

Wrap Up

As always, links to all the materials I referenced are available in the show notes or by going to theacidrefluxguy.com/005.

My name is Don Daniels aka The Acid Reflux Guy and this was another episode of The Reflux Cycle show. Signing off.

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Don is a best selling author of 'How I Cured My Silent Reflux,' and a former acid reflux sufferer for more than 15 years. With several family members with the disease, and a medically diagnosed hiatal hernia he resigned to the fact that he would take acid blockers for the rest of his life. Dissatisfied with medical advice, he researched the root causes of acid reflux and by solving them was able to eliminate his acid reflux for good!
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1 month ago

Don, I’ve been on Omeprazole 20mg once daily for more than 15 years for gerd reflux. With ppi side effects I decided to stop Omeprazole on 3/8/24. I am of course suffering with horrible rebound heartburn. So how long should I wait for rebound symptoms to stop to judge if my gerd has been healed? Should I wait a month or so before I begin Betaine HCI + Pepsin, if I feel I need it? Thank you for your feedback.

1 month ago
Reply to  Allison

Hey Allison, I’ve also been on 20mg of Omeprazole daily for over a decade. Just found out about Betaine a week ago. I quit my Omeprazole cold turkey two days ago and started taking Betaine (one 650mg pill per meal) that same day. I was expecting a lot of rebound symptoms in the beginning, but the change was immediate – 90% of the issue was gone during the day and I slept through the night with no issue. (I also limited my eating strictly to mealtimes.) I’m hoping the last 10% will be resolved over time as I build my… Read more »

6 months ago

I tired the link for the free digestion test…..”404!THE PAGE YOU WERE LOOKING FOR DOESN’T EXIST.”

Tammy Spurlock
Tammy Spurlock
8 months ago

Can i purchase the What to eat book – I want the book to hold in my hands – not on the internet! Can I do this?

Tammy Spurlock
Tammy Spurlock
8 months ago
Reply to  Don Daniels

I need the green sheets and all to tell me what to eat – I can’t even see it – I have tried enlarging it – no luck. Could I pay you to send me those yellow/green sheets so I can follow it.
Thank you!

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