Heartburn! Risks of Long Term Use of Acid Blocking Drugs

The health of the digestive system is in many ways one of the cornerstones of overall health and vitality. When there is ongoing inflammation, or other chronic issues affecting digestive tract function, it can pave the way for other downstream health concerns over time. It makes sense, as this system is where we break down the food we eat, absorb vital nutrients from that food, and then ultimately get rid of metabolic wastes on the other end. One of the most common digestive system issues that involve the upper GI tract is esophageal reflux disease (GERD), often referred to as “heartburn.” This condition is routinely treated with medications designed to eliminate the acidity of the stomach altogether.

Currently on the top 10 list of most prescribed medications, estimated at over 100 million prescriptions annually, is a class of stomach acid blocking drugs called proton pump inhibitors (PPIs). The two most popular drugs, Nexium and Omeprazole, are now available over-the-counter, making it very easy to self-prescribe and address esophageal reflux.

So, simply take a daily drug that eliminates stomach acid, and problem solved, right? Like many medications, this approach might manage discomfort short-term but fails to address the underlying causes of reflux and while doing so, compromises a very important part of the body’s overall digestive process. The stomach is meant to be very acidic, as this is necessary for the early stages of food digestion. Mineral absorption from mineral rich foods is particularly compromised by a non-acidic stomach, and long-term use of these medications results in deficiencies of crucial vitamins and minerals like iron, magnesium, calcium and B vitamins.

Research on this topic has suggested that long-term use (more than two weeks) of this class of drugs is contributing to poor health, and in some cases serious disease. Studies indicate an increased incidence of bone fractures from long term PPI use, as well as significant disturbances of the healthy and beneficial microbial gut flora, in some cases leading to dangerous C. difficile infections. Stomach acid provides a barrier to potentially harmful microbes, which is compromised by these meds.

One of the main arguments for PPI drug use has long been that the use of these medications may prevent esophageal cancers in those affected with GERD. A large Swedish study, though, suggested that the more consistent patients were with daily and long-term use of their PPI meds, the higher the incidence of esophageal cancers. There is also evidence that long-term use of these drugs may contribute to increased incidences of colon, pancreatic and liver cancers.

Studies also describe higher rates of chronic kidney disease (CKD), and several studies link long term PPI use to higher rates of dementia/ Alzheimers in the elderly. The downstream risks of nutrient malabsorption and the metabolic impact is evident in many body systems, to include evidence that even the cardiovascular system is negatively impacted by long-term PPI drug use.

As mentioned initially, the health of the digestive system is foundational to health, so it is no surprise that compromising its basic functions would have such dramatic effects. If PPI medications are not the answer to symptoms associated with GERD, what alternatives exist? The universal answer is this: Discover and address the underlying causes.

In most cases dietary triggers contribute to acid reflux. Eliminating dietary triggers can be a game changer. The tone of the esophageal sphincter, and other structural issues may also be a factor. Mental/emotional issues and stress can contribute as well. In many cases, particularly in elderly individuals, the problem can paradoxically be already-low stomach acidity levels causing reflux. The solution in these instances is counterintuitively improving stomach acid levels.

As you might imagine, it is ideal to have a holistic minded physician guide you through the process of discovering the underlying causes and potential dietary triggers while weaning you off PPI meds if appropriate– abrupt discontinuation of long term PPI use can cause unpleasant rebound heartburn symptoms. A judicious weaning program combined with implementing herbs and nutrients that help to heal inflamed and irritated digestive mucosa is typically the recipe for the successful removal of these drugs from the medicine cabinet.

Joshua Phillips, ND is a naturopathic physician and the director at Hawthorn Healing Arts Center in Bend, Oregon. He can be reached at docnaturecure@gmail.com with questions or comment.

This article appears in the Source December 18, 2025.