Stomach Acid: Friend or Foe?

Learn why Hydrochloric Acid (HCL) may be the cause of your GERD, Acid Reflux, Thyroid Problems, and Low Muscle Tone.

Far more Americans today face digestive issues such as constipation, foul smelling gas, and indigestion that are caused from having too little stomach acid than too much.12 It sounds a bit strange that having too little acid can cause heartburn doesn’t it?

Let’s find out what stomach acid is, how it is tied into stress, how to test levels, and go over strategies to normalize levels to better understand protein metabolism.

The Importance of Stomach Acid

Stomach acid is made in the stomach and consists mainly of hydrochloric acid or commonly referred to as HCL. This acid is very important to your health because is kills foreign invaders in our food, activates digestive enzymes, and stimulates muscle contractions.1 About 80% of protein digestion is completed in the stomach with HCL, pepsin, and gastrin. The rest is completed with pancreatic enzymes, intestinal enzymes, and bacteria in the large intestine.

Stomach acid should be strong enough to digest a nail! Acids are measured on the pH scale that ranges from 0 to 14. The lower the number, the more acidic the fluid. The pH of your stomach should be 1 to 2 the same as battery acid, which can dissolve steel.2

If the pH of the stomach is too high, then the enzymes will not be activated in the stomach and food will not be digested, leading to the putrefaction of proteins. This can lead to bad breath, stinky gas, and bacterial overgrowth.

Stomach Acid and Pepsin Levels Can Decline with Age

The results are mixed. One study estimated that 30% of U.S. men and women older than age 60 have atrophic gastritis, a condition in which too little acid is secreted by the stomach.5 Another study of 206 individuals also found that Pepsin (protein digesting enzyme made in the stomach) decreased by approximately 40% in the elderly but age did not affect stomach acid levels.

This same study concluded that lifestyle and diet were the #1 determining factor in the levels of stomach acid, even over the age of the individual.3

Stress Can Lower Stomach Acid

According to Dr. Tim Francis, chloride (from sodium chloride or table salt), magnesium, zinc, and B vitamins contribute to making stomach acid. Foods high in these vitamins and minerals include green leafy vegetables, mushrooms, liver, and sweet potatoes.16, 17

Your adrenal glands also use the same minerals to make the hormone cortisol. Cortisol controls blood sugar levels, regulates metabolism, reduces inflammation, and helps you think faster. Interestingly, stress induced by shock, massive burns, sepsis, or major trauma is also associated low stomach acid.4

Is Heartburn Caused from Low Stomach Acid?

Heartburn is a burning sensation in the chest that is caused by the recycling of bile (used to breakdown fats) through the stomach and sometimes into the lower esophagus, is another symptom of low stomach acid. Many people choose to suppress the stomach acid using over the counter antacids, alkalizers, or PPIs. This approach many times worsens the problem, causing long term problems such as parasitic infection, epithelial lining problems, inflammatory bowel disorders, and amino acid deficiencies. It is the opposite of what should be done to promote the natural acidic environment.12

Jonathan Wright, MD, states, “In 24 years, I’ve worked with thousands of individuals who’ve found the cause of their heartburn and indigestion to be low stomach acidity. In nearly all of these folks, symptoms have been relieved and digestion improved when they’ve taken supplemental hydrochloric acid and pepsin capsules.”

What Testing Should You Consider?

The Heidelberg Stomach Acid

The Heidelberg Stomach Acid Test is the gold standard test for measuring stomach acid. This test costs around $350, most insurance plans do not cover it. It uses a small capsule with a wireless electronic transmitter. This will determine if you have too much acid production called hyperchlorhydria or too little acid called achlorhydria.13

The test works by measuring the pH of the stomach after drinking small amounts of baking soda. Baking soda is sodium bicarbonate which reduces acidity and neutralizes the stomach acid. If the acid does not return to normal after drinking the baking soda, then that is a positive test for hypochlorhydria.14

Test Directions

  1. Do not take and acid suppressing drugs for at least 4 days before the test
  2. Fast for 12 hours (do not eat after dinner, do the test in the morning)
  3. Swallow the small electronic capsule with water
  4. Drink a solution of baking soda
  5. The test will record the time it takes to reacidify (pH of 1-3)

CMP Blood Test with Phosphorus

A doctor can diagnose low stomach acid levels off a comprehensive metabolic panel. Patient history and symptom analysis can also help round out the diagnosis and treatment plan. You will notice that most of the following markers are surrounding protein and the by-products of digesting protein. Be sure to ask for phosphorus as some CMP tests do not include it.

Low Phosphorus: If your phosphorus levels are low, than you are not breaking your protein down. Most phosphorus comes from dietary protein digestion. This is very important as phosphorus balances calcium in the body, if this gets too low, then you may experience kidney, gallstones, bone spurs, low bone mass, and calcium deposits.

Serum Protein: Since stomach acid is needed for protein digestion, when levels are under 6.9 or over 7.4 g/dl. 15

Globulin: levels under 2.4 or over 2.8 g/dL than it could be a sign of low stomach acid. According to Dr. Jockers, “Especially if liver enzymes (AST and ALT) are relatively normal.” 15

High BUN Levels: Urea is the major nitrogenous waste product. Nitrogenous waste products only relate to proteins since only proteins contain nitrogen. Low stomach acid may result in high amounts of nitrogenic waste in the blood stream. This may be seen as a Blood Urea Nitrogen (BUN) levels of 20 or higher.15

Test Directions

  1. Fast for 12 hours (do not eat after dinner, do the test in the morning)
  2. Drink plenty of water
  3. Go to doctor’s office or blood draw center to give blood
  4. Make appointment to review the results with your doctor

Does Stomach Acid Only Digest Protein?

No, stomach acid also supports the digestion and absorption of carbohydrates, fats, and fat-soluble vitamins (A, D, and E) by stimulating the release of pancreatic enzymes and bile into the small intestine.

The Thyroid-Stomach Acid Connection.

Stomach acid has a direct connection to thyroid function. Your thyroid runs the basil metabolic rate, or how fast your body uses energy, like keeping warm or breathing. If you are not digesting protein correctly with enough stomach acid and pepsin, your body will automatically slow itself down by down-regulating thyroid function. It does this to keep from metabolizing body tissues, like skin, muscle tissue, and organ tissue. Many people experience pitting of the muscle and low muscle mass if this is happening.

3 Ways to Safely Raise Your Stomach Acid Levels

  1. Hydrochloric acid and pepsin supplements have been used by thousands of physicians for decades and are considered a safe treatment for low stomach acid.
  2. Bitter herbs are gaining popularity for not only increasing stomach acid but also to increase bile acids. “The dried root of Gentiana lutea have been used as a digestive aid for centuries, especially in bitter tonics. Modern research has shown that gentian, which contains two of the most bitter substances known, the glycosides gentiopicrin and amarogentin, acts on taste bud receptors and cellular bitter receptor sites to stimulate stomach acid and bile secretion.” 11 Amazingly, according to Lee Carroll, bitters also help Esophageal Sphincter Dysfunction by resyncing the 8 bands of the stomach and the sphincters.
  3. But for long-lasting results, you must focus on diet. Eating lots of dark green leafy vegetables high in magnesium, seeds loaded with beneficial zinc, mushrooms high in B vitamins, and enzymatically rich fruits must be part of your daily regimen. Many doctors prescribe smoothie recipes based on the individual needs.

What to Do If You Have an Ulcer

The conventional treatment for helicobacter pylori infection or autoimmune metaplastic atrophic gastritis can also lower stomach acid levels.6 Conventional treatment typically includes repeated administration of acid-reducing agents, such as proton-pump inhibitors (PPIs) or H2-receptor antagonists (H2-RAs), commonly used to manage symptoms of gastroesophageal reflux disease (GERD) or peptic ulcer disease (PUD).

Individuals on daily drug regimens of acid-reducing agents therefore will have high gastric pH (3.5 or higher).7 Therefore, they cannot fully digest protein leading to many amino acid deficiency symptoms such as slow wound healing, bone fractures, hair loss, and pitting of the skin.

Individuals with an ulcer should treat the epithelial tissue with an ulcer supplement and herb plan before starting hydrochloric acid and pepsin enzyme supplements. Stomach acid can be quickly restored using betaine hydrochloride and Pepsin supplementation.9

After leaving the stomach, the hydrochloric acid is neutralized in the duodenum by sodium bicarbonate.10 If the pancreas is not strong enough to produce the sodium bicarbonate, then additional ulcerations of the duodenal can form. In this case, the individual should support the pancreas with herbs such as Gymnemia and minerals such as chromium from foods such as liver and nutritional yeast along with a low glycemic index diet.


I hope you can now have a better understanding of how low stomach acid may be the root cause of your digestive issues. Let’s sum up the main points of this article:

  • Stomach acid is very important to digesting proteins because of how it acidifies the stomach to activate the Gastrin and Pepsin enzymes.
  • Stomach acid also stimulates peristalsis or the muscle coordination of the intestines; so it helps with constipation!
  • It is much more common to have too low stomach acid than it is to have too high stomach acid.
  • The older you are the less likely you are making enough stomach acid and pepsin. Yet, the level of stomach acid is more dependent on lifestyle and diet than age.
  • Betaine Hydrochloride, pepsin enzyme supplementation, and bitter herbs are safe ways to normalize chronic stomach acid deficiency.
  • Testing is relatively non-invasive. Common blood tests like a Comprehensive Metabolic Panel with Phosphorus can be used to diagnose, but the gold standard is the Heidelberg Stomach Acid Test.

We recommend getting a free online digestive assessment and talk to a trained functional healthcare doctor to better understand your protein digestion. Find someone who is trained to utilize testing, whole food supplements, high quality herbs, and dietary strategies. It is also recommended to track your plan every couple of weeks.

Low stomach acid is a real thing that can be normalized! Learn about your digestive symptom patterns by getting a free assessment here. If your symptom patterns indicate that you have problems digesting protein, then you should sit down with your functional medicine doctor to better understand a plan to normalize your stomach acid.


1. Maton, Anthea; Jean Hopkins; Charles William McLaughlin; Susan Johnson; Maryanna Quon Warner; David LaHart; Jill D. Wright (1993). Human Biology and Health. Englewood Cliffs, New Jersey, USA: Prentice Hall. ISBN 0-13-981176-1.
2. Haas, Elson. “Digestive Aids: Hydrochloric acid”.
3. Feldman M1, Cryer B, McArthur KE, Huet BA, Lee E. Effects of aging and gastritis on gastric acid and pepsin secretion in humans: a prospective study. Gastroenterology. 1996 Apr;110(4):1043-52.
4. McGuigan J E. In: Harrison’s Principles of Internal Medicine. Isselbacher K J, Braunwald E, Wilson J D, Martin J B, Fauci A S, Kasper D L, editors. New York: McGraw–Hill; 1994. pp. 1363–1382.
5. Krasinski SD, Russell RM, Samloff IM, et al. Fundic atrophic gastritis in an elderly population. Effect on hemoglobin and several serum nutritional indicators. J Am Geriatr Soc 1986; 34:800-806.
6. Jonathan Wright, MD, The Digestive Theory of Aging, Part I,
7. El-Omar EM, Oien K, El-Nujumi A, Gillen D, Wirz A, Dahill S, Williams C, Ardill JE, McColl KE. Helicobacter Pylori Infection and Chronic Gastric Acid Hyposecretion. Gastroenterology. 1997;113:15–24. [PubMed] 8. Cohen S. Gastritis and Peptic Ulcer Disease. In: Albert RK, Cohen S, editors. The Merck Manual for Health Care Professionals. 19. Merck Sharp & Dohme Corp; Whitehouse Station, NJ: 2012. [accessed May 1: 2013]. [Online] Gastrointestinal Disorders.
9. Marc Anthony R. Yago,1 Adam R. Frymoyer,2 Gillian S. Smelick,3 Lynda A. Frassetto,4 Nageshwar R. Budha,3 Mark J. Dresser,3 Joseph A. Ware,3 and Leslie Z. Benet. Gastric Re-acidification with Betaine HCl in Healthy Volunteers with Rabeprazole-Induced Hypochlorhydria. Mol Pharm. 2013 Nov 4; 10(11): 4032–4037.
10. Maton, Anthea; Jean Hopkins; Charles William McLaughlin; Susan Johnson; Maryanna Quon Warner; David LaHart; Jill D. Wright (1993). Human Biology and Health. Englewood Cliffs, New Jersey, USA: Prentice Hall. ISBN 0-13-981176-1.
11. Bradley PR, ed. British Herbal Compendium (Vol. 1): A handbook of scientific information on widely used plant drugs. Guilford and King’s Lynn, Great Britain: Biddles Ltd; 1992:109- 111
12. Banoo H and Nusrat N. “Implications of Low Stomach Acid: An Update” RAMA Univ. J. Med Sci 2016;2(2): 16- 26
13. DePestel, D. D., Kazanjian, P. H., Cinti, S. K., Kauffman, C. A. and Carver, P. L. (2004), Magnitude and Duration of Elevated Gastric pH in Patients Infected with Human Immunodeficiency Virus After Administration of Chewable, Dispersible, Buffered Didanosine Tablets. Pharmacotherapy, 24: 1539–1545.
14. Stack BH. Use of the Heidelberg pH capsule in the routine assessment of gastric acid secretion. Gut. 1969;10(3):245-246.
15. Dr. Jockers: 5 Ways to Test Your Stomach Acid Levels.
16. World’s healthiest foods. Dietary reference intake for zinc., 2018.
17. Institute of Medicine. Dietary reference intakes for thiamin, riboflavin, niacin, vitamin B6, folate, vitamin B12, pantothenic acid, biotin, and choline. Washington, DC: National Academy Press, 1999.

Get Your Functional Digestive Assessment

Our 5-minute ‘yes’ or ‘no’ questionnaire will give you a 6-page educational report. Start your journey to feeling great, looking better, and living longer by addressing your digestive health.

Get Your Functional Digestive Assessment

Our 5-minute ‘yes’ or ‘no’ questionnaire will give you a 6-page educational report. Start your journey to feeling great, looking better, and living longer by addressing your digestive health.