Follow on

Cause Of Low Stomach Acid (Hypochlorhydria)

Low stomach acid or Hypochlorhydria is a deficiency of hydrochloric acid in the stomach. While excess stomach acid is commonly believed to cause indigestion, these days, it is being more readily accepted that low levels of stomach acid may actually be the cause. Stomach acid is made up of hydrochloric acid or HCL, enzymes, and a mucus coating that protects the lining of your stomach. Hydrochloric acid (HCL) helps your body break down, digest, and absorb nutrients such as protein and fat and having the proper levels helps eliminates harmful bacteria, yeast and viruses that hitch a ride on the foods we eat and cause many GI problems.

Transcript Jan 2021

In today’s video, I want to review some of the causes of Low stomach acid (hypochlorhydria). In previous videos I have talked about Symptoms of low stomach acid, natural treatment options for low stomach, I have talked about how to test for low stomach acid and while all of these are important- it equally important to understand what’s actually causing low stomach acid. How do you try to fix something if you don’t know what the cause is.

Hydrochloric acid helps your body to break down, digest, and absorb nutrients such as protein. It also eliminates bacteria and viruses in the stomach. Left untreated, low stomach acid can cause damage to the gastrointestinal (GI) system, cause infections like SIBO, fungal overgrowth, leaky gut. We also know that

Low Stomach Acid Is Also Associated With A Number Of Chronic Health Conditions, Including:

  • Small Intestinal Bacterial Overgrowth (SIBO)
  • Pernicious Anemia
  • H.pylori
  • Chronic Gastritis
  • Celiac disease
  • Asthma
  • Hypothyroidism
  • Autoimmune Thyroid disease (Hashimotos)
  • Food allergies
  • Chronic inflammation
  • Eczema
  • Grave’s disease
  • Gallstones
  • Rheumatoid arthritis

Most Common Causes for Low Stomach acid (Hypochlorhydria)

Cause Of Low Stomach Acid (Hypochlorhydria)

Atrophy of Gastric Mucosa

#1 on my list of causes for low stomach is atrophy of the gut/gastric mucosa. Atrophy is defined as anatomical changes that occur in the intestinal mucosa after chronic – Just like a muscle that has atrophied, our Gut lining can atrophy as well. This can be things due to the aging process or it can be due to inflammatory changes like ulcers, chronic gastritis infections, or it could be due to autoimmune diseases like I mentioned a moment ago celiac disease, and pernicious anemia.

The consequences of atrophy will include impaired absorption of nutrients and either a decrease in hydrochloric acid production or the inability to produce hydrochloric acid this is referred to as achlorhydria

Just for a moment, think about the consequences this can have on your body… if you cant break down proteins and fats, that means you may have all kinds of amino acid imbalances, you might have all kinds of essential fatty acid imbalances (omega 3’s and omega 6’s), you will be deficient in your fat soluble vitamins (ADEK) If you have low stomach acid you also often suffer with B12, Zinc, Copper, Calcium and Magnesium deficiency as well.

The consequences to these deficiencies may include things like depression, fatigue, low RBC count, might be things like brain fog, you might develop chronic pain due to vitamin D deficiency, you might have asthma and immune system problems due to low vitamin D, low vitamin A, you may develop gut inflammation due to low zinc levels. So hopefully you can see that this has a snowball effect on your health.

Vitamin Deficiency

Another common cause of low stomach acid is Vitamin deficiency. In the last video I said that low stomach acids can cause Deficiency of a variety of vitamins and minerals and this is true, but it turns out that vitamin deficiencies caused by inadequate dietary intake can also predispose you to low stomach acid. Deficiencies in zinc, chloride, and B vitamins may also lead to low stomach acid production. These deficiencies may be caused by inadequate dietary intake or by nutrient loss from stress, smoking, injury or insult to gastric mucosa as well as alcohol consumption. People with low stomach acid often need to supplement with calcium,vitamin D, Iron and B12.


Taking antacids or medications prescribed to treat ulcers and acid reflux, such as PPI’s and H2 receptor antagonists (Tagamet, Zantac, Pepcid), can also lead to low stomach acid/hypochlorhydria and often comes as a surprise to many people. Medications like oral contraceptives can lead to B12, B6 and folate vitamin deficiency.


Chronic stress decrease production of stomach acid leading to Hypochlorhydria. Here’s why- Have you ever heard of the Fight or Flight mechanism or Rest and Digest mechanism? These are the branches of your Nerve system- The Sympathetic and parasympathetic nerve system. During stress, we have an increase in our fight/flight hormones like adrenaline and cortisol this Is activated by our Sympathetic nerve system-

As you can imagine-if you are in fight/flight mechanism (that Sympathetic state), your body is not thinking about digestion is it? Your body is dealing with a threat- and so digesting food, releasing acid, and GI motility are not top priorities at the moment. This is also how stress is tied into not only things like low stomach acid, but many other Gastrointestinal symptoms related to IBS. Remember when it comes to digestion we want to be in that parasympathetic state- the rest and digest state. Chronic stress  may also decrease production and secretions of stomach acid leading to Vitamin deficiency.

stress and low stomach acid



H. Pylori is normal killed or kept in check by normal HCL production. Infection with H. Pylori is a common cause of gastric ulcers. If left untreated, it can result in low stomach acid and infections with H.Pylori are also associated with stomach cancer.

Low Thyroid or Hashimotos

The thyroid is a butterfly-shaped gland located in the neck. The thyroid gland is responsible for making hormones that regulate your body’s metabolism, which is the body’s process of creating and using energy. Although hypothyroidism can contribute to low stomach acid, low stomach acid can also contribute to hypothyroidism. It’s estimated more than 90 percent of the population suffers from hypochlorhydria, due to nutrition-poor diets of processed foods. Studies have found that people with Hashimoto’s and hypothyroidism often have low stomach acid or a more severe and advanced case called achlorhydria (lack of stomach acid). These digestive malfunctions that stem from low stomach acid sets the stage for autoimmune disease, chronic stress or poor absorption of nutrients, all of which could lead to hypothyroidism. If you have been struggling with chronic indigestion, GERD or other stomach or intestinal problems this could a warning sign that you may have undiagnosed hypothyroidism.


Surgeries of the stomach, such as gastric bypass surgery, can reduce production of stomach acid leaving you in a state of hypochlorhydria.

Autoimmune Disease-

Pernicious anemia is an autoimmune disorder where the immune system destroys two kinds of cells. The first… are the parietal cells- These are the cells that produce stomach acid and the 2nd cell is intrinsic factor. Intrinsic factor binds to B12 and is needed to help with the absorption of B12 into the bloodstream. If you continue to have low levels of B12, We suggest testing for pernicious anemia and Intrinsic factor. Both of these antibodies can be tested for in the blood. When acid levels in the stomach are low the stomach cannot digest food thoroughly. If you test positive for either of these, the end result will be low stomach acid and gut atrophy.

Pernicious Anemia and low stomach acid


When suspecting achlorhydria, multiple tests are conducted to confirm the diagnosis and to find its primary cause:

  • Antiparietal and anti-intrinsic factor antibody
  • Biopsy of stomach
  • Gastric pH monitoring
  • Serum pepsinogen level (a low serum pepsinogen level indicates achlorhydria)
  • Serum gastrin levels (high serum gastrin levels greater than 500 to 1000 pg/mL may indicate achlorhydria)
  • Tests for detecting H. pylori infection (urea breath test, stool antigen test, biopsy, polymerase chain reaction-PCR or fluorescent in situ hybridization [FISH])
  • Hemoglobin level

Functional Medicine Consult

Other Videos Recommended By Our Readers.


See Other Recent Post!

Creating health doesn't have to be a guessing game!

Our Team will help you harness your health so you can trust your body and feel like YOU again. We can help find your Root Cause.