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A Functional Medicine GERD Protocol

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A Functional Medicine GERD Protocol

It was initially thought that most gastroesophageal reflux disease (GERD) was caused by excess stomach acid ("hyperchlorhydria"). This is likely why over 15 million Americans manage their GERD symptoms with a proton pump inhibitor (PPI), a pharmaceutical medication that inhibits stomach acid secretions. However, we now understand that GERD is seldom caused by the production of too much stomach acid. Your PPI may actually be contributing to GERD, along with causing nutrient deficiencies, opportunistic infections, and certain chronic diseases. (3)

There are other treatment options to explore if you are one of the 20% of Americans that struggles with GERD (1). This article will discuss the physiologic mechanisms that can contribute to GERD and the diagnostic and treatment considerations that play into an integrative GERD approach.


What is GERD?

GERD is the frequent reflux of stomach contents into the esophagus, associated with uncomfortable upper digestive symptoms. It often results in esophageal inflammation (called esophagitis) and can lead to serious complications, including narrowing of the esophagus and precancerous changes to the esophageal cells. (2)

During normal digestion, food travels down the esophagus and is let into the stomach by the relaxation of a muscular band called the lower esophageal sphincter (LES). The LES then closes, creating a tight barrier between the esophagus and the stomach, preventing the regurgitation of stomach contents into the esophagus. In GERD, various factors can lead to LES dysfunction and inappropriate reflux. (4, 13)

The terms GERD, reflux, and heartburn are often used interchangeably, but they do have subtle differences in meaning (1):

  • Reflux: The backward flow of gastric contents into the esophagus
  • GERD: The disease defined by frequent reflux
  • Heartburn: A symptom of GERD, described as a burning sensation in the chest

Factors that may increase your risk for developing GERD include (3):

  • Connective tissue disorders, like scleroderma
  • Hormonal imbalances in estrogen and progesterone
  • Conditions that delay stomach emptying, like viral infections, vagal nerve damage, diabetes, and autoimmune disease
  • Eating the Standard American Diet (SAD) or eating large meals late at night
  • Tobacco use
  • Consumption of alcohol and coffee
  • Age greater than 40 years

Use of the following medications is also associated with an increased risk of GERD (2):

  • Antidepressants
  • Albuterol (i.e., "rescue inhaler")
  • Anticholinergic medications that are prescribed for various conditions, including respiratory disorders, cardiovascular disease, and urinary incontinence
  • Benzodiazepines, often prescribed for anxiety, seizures, and insomnia
  • Calcium channel blockers, used to lower blood pressure
  • Nitroglycerin, used to prevent chest pain caused by heart disease
  • Non-steroidal anti-inflammatory drugs (e.g., aspirin and ibuprofen)

GERD Symptoms

The most typical symptom of GERD is frequent heartburn resulting from recurrent acid reflux that irritates the esophagus. Heartburn pain typically travels upward behind the chest bone towards the mouth. With more severe reflux, patients may report regurgitation of food into the throat and a sour taste in the mouth. Acid reflux and heartburn are generally worse after meals and with lying down. (4)

GERD can also present with other symptoms, including (2):

  • Difficulty and pain with swallowing
  • Burping
  • Nausea
  • Upper abdominal pain
  • Chronic cough
  • Asthma
  • Dental erosions
  • Hoarseness of voice
  • Lump-in-the-throat sensation

What Causes GERD?

The origins of GERD can be multifactorial and complex but typically involve LES dysfunction that causes transient relaxation of the sphincter. Many aspects of the Western lifestyle can contribute to this relaxation, including lack of complete chewing, lying down too soon after a meal, eating large meal portions, excessive saturated fat and alcohol intake, and smoking. Increased intra-abdominal pressure associated with obesity and pregnancy can contribute to LES laxity by exerting too much upward pressure onto the sphincter. (13)

Hiatal hernia occurs when the stomach travels upward from its appropriate position in the abdomen and bulges through the diaphragm (the muscle separating the chest and abdomen). A hiatal hernia can put excessive pressure on the LES and induce increased muscle laxity.

Hypochlorhydria, or low stomach acid levels, is a major and often overlooked cause of acid reflux and GERD. Stomach acidity helps to control LES function. When LES sensors detect an acidic stomach environment, the muscles constrict, closing the sphincter. In states of low stomach acid, this feedback mechanism does not occur, inducing LES relaxation and allowing stomach contents to travel into the esophagus. Conventional medications used to treat GERD contribute to hypochlorhydria and worsen digestive issues. So, differentiating between high and low stomach acid as an underlying cause of GERD is an essential step in the GERD diagnostic process. (3, 7)

Small intestinal bacterial overgrowth (SIBO) is the overgrowth of bacteria in the small intestine and, in more severe cases, the stomach and esophagus. Evidence suggests that SIBO is prevalent in the GERD population and can contribute to GERD-like symptoms, including heartburn, abdominal pain, and burping. Additionally, PPI use and hypochlorhydria are risk factors for SIBO development. This means SIBO can occur due to GERD treatment protocols and exacerbate digestive symptoms. (9-11)

Bile reflux occurs when bile, a digestive liquid produced by the liver to aid in the digestion of fats, backs up into the stomach and esophagus. It can occur on its own or in conjunction with acid reflux.

GERD can be associated with eosinophilic esophagitis (EOE), an infiltration of the esophageal tissues with eosinophils, a type of white blood cell. Food allergies are known to cause eosinophilia (an elevation in eosinophils) and can cause transient relaxation of the LES in susceptible patients. In one study, 77% of children with EOE had identifiable food allergies, and esophageal inflammation and EOE symptoms improved greatly with the elimination of allergens from the diet. (5, 6)

Functional Medicine Labs to Test for Root Cause of GERD

Upper endoscopy: is routinely ordered in the diagnostic workup of GERD. Endoscopy is an imaging technique that can visualize the anatomy of the upper digestive tract, assessing for signs of hernia and esophagitis. Biopsies will often be taken during the procedure to rule out EOE and changes to esophageal cells indicative of disease complications. (12) Different techniques can be utilized to measure LES functionality and stomach acidity, including esophageal manometry, aspiration tests, and intragastric pH measurements. These are important tools in identifying hyperchlorhydria, hypochlorhydria, and bile reflux as contributors to disease pathology. (12)

A 3-hour breath test: can be performed at home to diagnose SIBO.

Food allergies: are typically diagnosed by skin prick testing or blood panels measuring the IgE allergic immune response to food allergens. Food allergies should especially be ruled out if eosinophilia is diagnosed with a biopsy.

Food sensitivities: The research supporting food sensitivities in the development of GERD is not as strong, but sensitivities certainly can exacerbate gastrointestinal inflammation and make the healing process more difficult. A food sensitivity panel can screen for foods irritating inflamed tissues and GERD symptoms.

Conventional Treatment for GERD

Doctors routinely rely on medications like antacids, histamine H2 receptor blockers, and PPIs that neutralize and inhibit stomach acid secretion. Patients may require surgery if they have severe symptoms or disease complications despite pharmacologic therapies.

Functional Medicine Treatment for GERD

Understanding that pharmacologic therapies come with risks, especially when used for prolonged periods, functional doctors avoid prescribing medications by addressing the underlying causes by modifying intraabdominal pressure, enhancing stomach emptying, and supporting lifestyle modifications while using alternative natural supplements to heal inflamed esophageal tissues.


Counseling on eating hygiene is essential to nutritional changes in GERD therapy. Eating small meals, avoiding lying down after eating, and eating the last meal of the day at least three hours before bedtime can all help to prevent reflux. (8)

Food trigger avoidance can reduce inflammation in the digestive tract and support the healing of inflamed tissues. Eliminating identified food allergies and sensitivities with an elimination diet is commonly recommended by functional practitioners. Other foods that typically trigger GERD symptoms include citrus fruits, onion, garlic, dairy, gluten, spicy foods, tomato, mint, chocolate, and coffee (8).

The severity of GERD symptoms can be impacted by the carbohydrates we eat. Eating simple carbohydrates (e.g., refined sugar, desserts, white rice, and bread) can contribute to LES relaxation, contributing to heartburn. In contrast, complex carbohydrates and fiber (e.g., vegetables, whole grains, beans) can relieve symptoms by absorbing stomach liquids and encouraging stomach emptying.

Complementary and Alternative Medicine

Research demonstrates that there are many supplemental options effective at treating GERD:

  • Licorice root soothes inflamed tissues, enhances stomach mucus secretion, and supports the healing of ulcers. In this randomized, double-blind study, patients with heartburn experienced a significant reduction in symptom scores after just 15 days of supplementation.
  • A 2020 systematic review concluded that probiotics ranging in doses from 1-46 billion CFU of various strains for up to 12 weeks significantly reduce reflux, nausea, heartburn, and belching.
  • Melatonin is a beneficial supplement for GERD for many reasons. Melatonin can prevent LES relaxation and esophageal injury caused by reflux. Symptom outcomes are improved in patients taking melatonin combined with omeprazole compared to those taking omeprazole alone.
  • Intake of dietary folate, vitamin B2, and vitamin B6 is associated with decreased risk of developing reflux esophagitis. Additionally, PPI use is associated with vitamin B12 deficiency. Taking a B vitamin complex can prevent PPI-induced nutrient deficiency and GERD-related complications.
  • Fumaria officinalis (fumitory) is a cholagogue, an herb that supports bile flow. In practice, Fumaria significantly improves GERD symptoms, likely due to its ability to prevent bile reflux and enhance LES function.

When applicable, treating SIBO with natural and pharmaceutical antibiotics and probiotics can restore the balance of the upper intestinal microbiome, relieving GERD symptoms. Protocols encouraging the reduction and discontinuation of GERD medications will increase the efficacy of SIBO treatment plans and prevent SIBO recurrence.

Acupuncture with or without electrostimulation shows much promise for improving GERD. Research has shown that acupuncture can modulate stomach acid secretion, stimulate stomach emptying, and treat many gastrointestinal symptoms.

Improving peristalsis (muscle contractions that move intestinal contents downward) supports healthy digestion, prevents SIBO, and prevents reflux. Limonene and ginger are two natural supplements that are proven to support intestinal motility. Additionally, stimulating the vagus nerve with singing, humming, gargling, and yoga can support gastrointestinal motility and balance digestive secretions.

Supplemental digestive enzyme formulas that support digestion can improve GERD, especially in patients with hypochlorhydria and bile reflux. Natural supplements like apple cider vinegar and bitter herbs (e.g., dandelion, gentian) have also been shown to support stomach acid levels and liver function. (3, 7)

Lifestyle Modifications

Lifestyle modifications are a key component in managing GERD and should be incorporated into any GERD treatment plan. Despite the lack of extensive clinical data to support lifestyle modification efficacy as sole therapy, patients experience symptom relief and prevent recurrence by incorporating multiple changes into their daily routines. This study concluded that patients with reflux esophagitis experienced greater improvement in quality of life when utilizing lifestyle changes in combination with their PPI compared to those who did not.

The most common lifestyle modifications studied for GERD include weight loss, head-of-bed elevation, and avoidance of tobacco, alcohol, and late-night meals. Avoiding tight, restricting clothing and belts, especially during mealtimes, is another modification suggested to decrease intraabdominal pressure and prevent reflux. (8)


GERD is a multifactorial upper digestive disease that can cause significant health repercussions. Conventional therapy relies on pharmaceuticals to prevent acid reflux and heal inflamed tissues. Unfortunately, these may not address the root cause of the disease and can lead to additional health complications.

Functional doctors are trained in ordering and interpreting imaging and testing to understand the root cause of GERD. Integrative approaches emphasizing lifestyle modifications and natural supplements can effectively correct dysfunctional digestive patterns contributing to GERD and prevent the excessive use of pharmaceutical medications.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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Lab Tests in This Article


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10. Haworth, J., Boyle, N., Vales, A., et al. (2021). The prevalence of intestinal dysbiosis in patients referred for antireflux surgery. Surgical Endoscopy and Other Interventional Techniques, 35(12), 7112–7119.

11. Compare, D., Pica, L., Rocco, A., et al. (2011). Effects of long-term PPI treatment on producing bowel symptoms and SIBO. European Journal of Clinical Investigation, 41(4), 380–386.

12. Patti, M. G., MD. (n.d.). Gastroesophageal Reflux Disease Workup: Approach Considerations, Upper Gastrointestinal Endoscopy, Esophageal Manometry.

13. Rosen R.D., Winters, R. (2022, July 4). Physiology, Lower Esophageal Sphincter. StatPearls Publishing.

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