top of page

Underlying Causes of Acid Reflux

Updated: Mar 9, 2023

In the medical world, the underlying cause of acid reflux is generally overlooked and treatment is focused on band-aid solutions such as acid blocking medications. The problem with these medications is that they often stop working after a period of time, and lead to further digestive issues when used long-term. Overcoming acid reflux for good means understanding why you have acid reflux in the first place. This blog post will discuss the leading underlying causes of acid reflux, testing and natural treatment approaches.

Here’s a breakdown of what we will cover:

  • What are acid reflux, GERD and heartburn and how can you tell the difference?

  • What is the antireflux barrier

  • The importance of stomach acid and why you likely DON’T have too much

  • Causes of acid reflux and GERD

  • Testing for the functional underlying causes of acid reflux

What is acid reflux?

The lower esophageal sphincter, which is a muscular band at the base of the esophagus works together with the diaphragm like a valve to narrow and widen the esophagus. Their role is to relax during eating to allow food to enter the stomach and then contract afterwards to prevent the content of the stomach from coming back up into the esophagus and throat.

When these sphincters fail and stomach acid and food reflux back up into the esophagus and throat, this is what we call ‘acid reflux’. The symptoms of acid reflux include:

  • Heartburn.

  • A burning sensation or bitter taste at the back of the throat, sometimes with regurgitation of food.

  • A general complaint of stomach discomfort such as nausea after eating, burping, bloating, and upper abdominal discomfort.

What is GERD?

Gastro Esophageal Reflux Disease is a more severe, chronic form of acid reflux. Generally it is accepted that if you suffer from acid reflux more than twice a week you have GERD, but often it happens more frequently than that. The symptoms of GERD are the same as acid reflux but in addition you may have a cough, laryngitis, chest pains, asthma or poor sleep.

What is the antireflux barrier?

The lower esophageal sphincter (LES), the diaphragm, the phrenoesophageal ligament (a ligament that attaches the esophagus to the diaphragm) and the gastroesophageal junction (GEJ) are the main components of the antireflux barrier. The GEJ is like a flap-valve that works with the LES to stop reflux.

The antireflux barrier not working properly is considered to be the main underlying cause of acid reflux. Ironically, the LES requires sufficient amounts of stomach acid to remain closed, and too little stomach acid can potentially lead to acid reflux and GERD, despite the main treatment for these conditions being medications to reduce stomach acid production.

Why stomach acid is important

Stomach acid plays a very important role in digestion by breaking down food particles and killing unwanted pathogens before they can enter other systems of the body.

When we think about food and start to get hungry, this triggers secretions of stomach acid ready for digestion. Food that has been chewed and swallowed is further broken down by stomach acid

Stomach acid plays an important role in digestion and our immune system. Not only does it break down food particles, but it can also kill unwanted pathogens and prevent them from entering other systems of the body. Food that has been chewed and swallowed is further broken down by stomach acid, in the ‘churning and burning’ stage of digestion.

The gastric juice, often referred to as stomach acid is very acidic and made up of a number of components throughout the upper GI tract, including:

  • Hydrochloric acid (HCl) - secreted by the parietal cells in the stomach.

  • Amylase - from saliva, breaks down carbohydrates before they hit the stomach.

  • Pepsin - digestive enzymes produced in the stomach that break down proteins. Pepsin is activated in an acidic environment.

  • Gastric lipase - produced in the stomach and helps break down fats.

  • Intrinsic factor - helps your body absorb vitamin B12.

Hydrochloric acid (HCl), which makes up the majority of stomach acid, has a pH range of 0.5 to 3.0. This is what HCl does:

  • Kills bacteria and other bad bugs in the food you eat. Levels below pH 3 are able to kill E. coli and H. pylori, amongst others.

  • Stimulates the closure of the LES (lower esophageal sphincter) which is critical to preventing acid reflux and GERD from occurring.

  • Activates the release of the enzyme, pepsin. When pepsin is released into the stomach it breaks down proteins into their smaller forms of amino acids and peptides. These processes aid the digestion of protein molecules throughout the rest of the GI tract.

  • Triggers the release of lingual lipase (in the mouth) as well as gastric lipase (in the stomach), an enzyme that helps break down fats into smaller molecules.

  • Has the ability to convert minerals into absorbable nutrients for the body’s use. Low HCl secretion decreases the bioavailability of nutritionally important minerals, such as iron, zinc, and calcium, making them more difficult to be absorbed and utalised.

The relationship between low stomach acid and acid reflux

Low stomach acid can lead to acid reflux through two different mechanisms:

> Low stomach acid and the antireflux barrier - High stomach acidity creates pressure on the LES which closes to prevent acid entering the esophagus and causing symptoms. The LES acts like a muscle and without sufficient stomach acidity, can become weak and less effective overtime.

> Low stomach acid and intra-abdominal pressure - Low stomach acid can create an environment that allows bacteria to overgrow in the GI tract. If this occurs, certain carbohydrates are likely to be fermented by the bacteria (their main fuel source) which leads to excess gas as a byproduct of the fermentation (particularly in the upper part of the small intestine), leading to increased pressure in the stomach (bloating). Additionally, if stomach acid is low, this can lead to putrefaction of undigested proteins, often after eating meat. This is because stomach acid is essential to break down proteins. When not broken down properly, these proteins begin to rot and produce excess gas in the stomach, leading to increased intra-abdominal pressure.

Other contributing causes of acid reflux

Outside of low stomach acid, there are some other contributing causes of acid reflux that are worth mentioning:

Medications: some prescription medications can have heartburn as a side effect because of their impact on the function of the LES.

Scleroderma (systemic sclerosis): a rare autoimmune condition where the body attacks the connective tissue and creates a thickening and hardening of the skin/tissue. If present in the esophagus, the LES’s function can become impaired.

Pregnancy: hormones that relax the muscles during pregnancy can also relax the LES.

Obesity. While obesity can’t cause acid reflux or heartburn directly, it can be a risk factor. It is thought that pressure from adipose tissue around the abdomen pushes the esophagus into the chest cavity forming a hiatal hernia. Obesity is also thought to cause the LES to relax.

Hiatal hernia - With a hiatal hernia, part of the stomach pushes into the chest cavity. It enters via an opening where the esophagus passes on its way to the stomach, preventing the LES from closing. It is usually caused by a weakness of the diaphragm muscle, but not everyone who has a hiatal hernia develops acid reflux or GERD.

Pregnancy - In later stages of pregnancy the growing fetus can put pressure on the mother’s abdomen and diaphragm, forcing stomach contents back up toward the esophagus.

Causes of Low Stomach Acid

The next step in understanding where your acid reflux is coming from is identifying what is contributing to low levels of stomach acid. These are the most common causes of low stomach acid:

H.pylori - If Helicobacter pylori bacteria manages to colonise in the stomach, it produces ammonia as a by-product. Ammonia is an alkali that neutralises stomach acid. In addition, H.pylori can inhibit acid production directly as well. Given that up to 50% of the population is thought to have H.pylori, it’s no wonder we have an ever-growing number of acid-reflux sufferers.

Age - As we age our gastric acid secretions become less. This is why GERD is a condition often associated with older populations.

Stress - Chronic stress, including extended strenuous exercise, psychological stress or other prolonged period of stress is a common cause of low stomach acid. Stress impacts the production of stomach acid via the ‘fight or flight’ nervous system, where digestive processes including stomach acid production can be switched off as your body focuses on dealing with the stress.

Vitamin or mineral deficiencies - zinc and vitamin B6 are essential for the production of Hydrochloric acid and deficiencies in either may lead to low stomach acid. Zinc deficiency is very common, particularly in women taking the oral contraceptive pill, which depletes zinc levels.

Proton pump inhibitors and antacids - These medications are specifically designed to reduce the volume and acidity of stomach acid and are commonly used to treat acid reflux. They often work initially, but long-term use can actually cause acid reflux by reducing sterilisation of pathogens (leading to bacterial overgrowth), and by inhibiting the antireflux barrier which requires high acidity to function properly.

GI surgery - Surgical procedures, such as gastric bypass surgery, can reduce the amount of stomach acid produced.

Ruling out underlying causes with testing

Effective treatment requires identifying the underlying cause/s of acid reflux. There are specific tests available that can help do this.


Ideally we would get a baseline on stomach acid, however there is no easy way to test your stomach acid levels without a specialist test called the Heidelberg Stomach Acid Test, which is reasonably invasive. The test involves swallowing a radio-transmitter capsule which reports pH levels in the stomach and needs to be ordered by a gastroenterologist.

However, there are other more easily accessible tests available which can provide markers that may indicate low levels of gastric juices. Comprehensive stool testing report on fat and protein malabsorption, and because we need sufficient stomach acid to effectively breakdown protein and fat, these markers can help to determine if low stomach acid is a problem.


Even if low stomach acid is suspected, the real question is WHY are stomach acid levels low? Outside of chronic stress, H.pylori, other GI pathogens and SIBO are the most common underlying causes which need to be ruled out and treated if necessary.

Although 50% of the population have H.pylori and may not be symptomatic, in symptomatic individuals, treating it can help to reduce symptoms.


SIBO (Small Intestinal Bacterial Overgrowth) leads to excess gas production in the small intestine which can result in increased intra-abdominal pressure. This pressure can cause the valve at the top of the esophagus to open up and result in acid reflux. Having SIBO ruled out as an underlying cause is an important step for anyone struggling with acid reflux.

Next steps

If you’ve made it this far, I hope you’ve learnt a lot about the actual underlying causes of acid reflux. If you have been struggling with acid reflux symptoms and you would like to get tested and have a personalised healing protocol developed specifically for you, please get in touch. I’d love to help you to overcome this. Start by scheduling a free 20 minute introductory consultation here.

197 views0 comments


bottom of page