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A Functional Medicine GERD Protocol: Testing, Nutrition, and Supplements

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A Functional Medicine GERD Protocol: Testing, Nutrition, and Supplements

Gastroesophageal reflux disease (GERD) is one of the most common gastrointestinal disorders, affecting up to 28% of North Americans. Not only does it cause uncomfortable symptoms and potentially severe health complications, but it also causes a significant economic impact. Estimated direct and indirect costs related to the disease total $10 billion annually. (1)

The conventional approach to treating GERD involves acid-blocking medications. Standard medications can be effective for some, but in most cases don't address the root cause of the problem and only provide temporary relief. It is estimated that up to 40% of people using standard treatment for GERD still exhibit symptoms. Additionally, prolonged use of these medications can increase the risk of nutrient deficiencies, opportunistic infections, kidney disease, certain cancers, heart attacks, and bone fractures. (2, 3)

These statistics suggest that alternative approaches to successful GERD treatment are warranted. This article will discuss a functional medicine approach to treating GERD, involving specialty testing, dietary and lifestyle modifications, and natural supplements.


What is GERD?

GERD, or gastroesophageal reflux disease, is defined by frequent reflux, the backward flow of stomach contents into the esophagus. Based on the endoscopic and histopathologic appearance of esophageal tissues, GERD is classified into three different phenotypes:

  • Non-erosive reflux disease (NERD): the most prevalent type of GERD seen in 60-70% of patients, characterized by the absence of esophageal mucosal injury (3, 4)
  • Erosive esophagitis (EE): characterized by damage to the esophageal lining, accounting for 30% of GERD cases (3)
  • Barrett's esophagus (BE): affecting 6-12% of patients, chronic GERD leads to the replacement of esophageal tissue with tissue that is similar to the lining of the intestine; BE increases the risk of esophageal cancer (4, 5)

GERD Symptoms

Clinically, GERD most commonly manifests with heartburn (a burning sensation in the chest) and regurgitation of food/fluids into the esophagus. These symptoms often worsen at night, after meals, and with lying down. Patients may present with other symptoms, including (2-4):

  • Chest pain
  • Dental erosions
  • Chronic cough
  • Laryngitis (hoarseness of voice)
  • Asthma
  • Difficulty and pain with swallowing
  • Lump-in-the-throat sensation
  • Burping
  • Nausea

What Causes GERD?

Multiple mechanisms can be responsible for the development of GERD. The problem is often linked to dysfunction of the lower esophageal sphincter (LES), the band of muscle at the junction between the esophagus and stomach. Usually, the LES remains closed except when you swallow, opening to allow food and liquids to pass into the stomach. The LES stays open for about five seconds after swallowing and then closes again to keep food and digestive enzymes from refluxing into the esophagus. Impairment in LES muscle tone and transient LES relaxation significantly contribute to reflux and GERD. When the sphincter is not closed tightly, esophagus and stomach compartmentalization is lost, and reflux can occur more easily. (4, 6)

Many aspects of the Western lifestyle are linked to an increased risk of LES dysfunction, including lack of complete chewing, eating large meal portions, lying down too soon after eating, excessive fat and alcohol intake, and smoking. Anything that puts persistent and intense pressure on abdominal muscles and gastrointestinal structures, including obesity and pregnancy, can induce LES laxity and increase the risk of hiatal hernia. Hiatal hernias occur when the stomach travels upward and through the opening in the diaphragm, reducing the integrity of the LES and contributing to GERD development. (7)

Stomach acidity is an important regulator of LES function. When LES sensors detect an acidic stomach environment, the sphincter muscles constrict to close the sphincter and prevent reflux. In a hypochlorhydric state, there is insufficient acid in the stomach, and this feedback mechanism does not occur, inducing a chronic state of LES relaxation. Many things can cause hypochlorhydria, including aging, regular use of antacids and acid-blocking medications, H. pylori infection, chronic stress, and gastric bypass surgery. This is important because conventional standards of care recommend using acid-blocking drugs to treat GERD, which further reduces stomach acidity. For those with GERD caused by hypochlorhydria, these medications exacerbate the problem. (7)

Impaired upper gastrointestinal motility is implicated in the development of GERD. Wave-like muscle contractions, called peristalsis, are responsible for clearing contents from the esophagus. Poor esophageal peristalsis is linked to reduced clearance of gastric reflux, severe reflux symptoms, and esophageal mucosal damage. Delayed gastric emptying, called gastroparesis, can also contribute to GERD by increasing pressure within the stomach, distending the stomach, and increasing exposure to stomach refluxate. (4)

Small intestinal bacterial overgrowth (SIBO) is the overgrowth of bacteria in the small intestine and is a common cause of heartburn, abdominal pain, and burping. Evidence suggests that SIBO is prevalent in patients with GERD and is more prone to develop with acid-blocking proton pump inhibitor medications and hypochlorhydria. (7)

Functional Medicine Labs to Test for Root Cause of GERD

Functional medicine labs help providers get to the root cause of symptoms and personalize treatment plans for patients suffering from GERD. Below are some of the labs you may consider ordering during a diagnostic evaluation of GERD.

Comprehensive Gastrointestinal Assessment

Understanding the gut's health, function, and microfloral composition is critical in managing and treating GERD. An upper endoscopy with biopsy is routinely ordered for patients with chronic GERD to visualize the anatomy of the upper digestive tract and rule out EE, BE, and other diseases that can present with GERD-like symptoms. Motility and intragastric acidity studies can also be ordered to measure LES functionality and stomach pH. (4)

Specialty tests that can assess digestive function, dysbiotic and infectious patterns, intestinal inflammation, and the need for digestive support include a comprehensive stool test, SIBO breath test, and Candida stool culture. These tests are beneficial in identifying factors contributing to GERD development and severity.

Food Sensitivities

Certain food triggers are known to exacerbate GERD symptoms by irritating the inflamed esophageal tissues, and many foods have been implicated in GERD pathogenesis. As such, dietary modification is often proposed as a first-line treatment in the conventional and functional medicine realms. A five-year retrospective study found that over 90% of patients with GERD were intolerant to at least five food items, most commonly milk, lettuce, coffee, brewer's yeast, pork, tuna, rice, sole, asparagus, and eggs. Food sensitivity and allergy testing can identify foods the patient is adversely reacting to so that the diet can be modified to eliminate an individual's specific trigger foods.

Hormonal Assessment

Acute and chronic stress can impair gastrointestinal motility and contribute to hypochlorhydria. Assessing adrenal function by measuring salivary cortisol and DHEA looks for imbalances in the body's stress response and helps to personalize the treatment approach.

Studies have shown that fluctuations and imbalances in female hormones, estrogen and progesterone, contribute to GERD by negatively affecting intestinal motility and LES function through the hormones' effects on receptors in the gastrointestinal tract (8, 9). A comprehensive female hormone panel screens for imbalances in these hormones.


Conventional Treatment for GERD

The conventional algorithm for treating GERD involves various stages of lifestyle modifications, pharmacologic therapy, and surgery. Lifestyle modifications, which are also emphasized in a functional medicine approach to treatment, include head-of-the-bed elevation, dietary changes, smoking cessation, and central/abdominal weight reduction. Pharmacologic medications include as-needed and scheduled antacids, histamine (H2) blockers, and proton pump inhibitors (PPIs). Surgery may be required in patients with severe, unresponsive symptoms, hiatal hernia, erosive esophagitis, or other disease complications. (10)

Functional Medicine Treatment Protocol for GERD

A functional medicine approach to treating GERD involves a root cause approach to addressing underlying factors contributing to reflux, making diet and lifestyle modifications, and using natural supplements to alleviate painful heartburn. Often, using complementary and integrative modalities allows patients to avoid or discontinue pharmacologic medications that, with time, come with a host of adverse side effects.

Therapeutic Diet and Nutrition Considerations for GERD

Eating hygiene (how we eat) can significantly impact GERD symptoms and reflux. Sitting down to eat, chewing slowly, and listening to hunger signals puts the body in a parasympathetic state, encouraging healthy digestive secretions and intestinal motility. Eating small meals, staying upright after eating, and eating the last meal of the day at least three hours before bedtime prevents reflux (7).

Avoiding GERD food triggers, commonly including citrus fruits, onion, garlic, gluten, spicy foods, tomato, mint, chocolate, and coffee, can reduce esophageal inflammation, support the healing of damaged tissues, and relieve heartburn (7).

A customized 4-6 week elimination diet based on food sensitivity results may be recommended as a personalized approach to trigger avoidance. All identified food sensitivities are strictly removed from the diet during an elimination. After the elimination period, foods are challenged back into the diet individually to observe for adverse responses. Each challenge should be performed over three days. On day one, the patient is instructed to eat one serving of the chosen food three times throughout the day. The patient should then avoid eating the food while observing for GERD symptoms on days two and three. All foods that trigger symptoms should continue to be avoided, but foods successfully challenged without causing symptoms can be reincorporated into the diet.

Paleo, Nutritarian, Whole 30, and Pegan diets are commonly recommended by functional medicine providers for patients with unidentified food sensitivities to encourage the consumption of healing, anti-inflammatory foods. (2)

Supplements Protocol for GERD

Supplements can effectively be used as an alternative to or in conjunction with pharmacologic therapy to heal inflamed tissues and palliate symptoms. Supplements should be chosen based on the desired mechanism of action to correct identified imbalances contributing to GERD. The following supplements can be considered for any patient with GERD, regardless of the underlying cause of the disease.

GI Relief

Thorne's GI Relief is a botanical blend of aloe vera, slippery elm, marshmallow root, and licorice (DGL) extract. These gut-healing herbs soothe esophageal irritation, calm gastrointestinal mucus membranes, and ease digestive discomfort. In a 2019 study, DGL and slippery elm significantly improved gastric and intestinal irritation.

Dose: two capsules before every meal and two capsules before bed on an empty stomach

Duration: 8-12 weeks

Heartburn Advantage

Heartburn Advantage is a formula by Integrative Therapeutics that combines zinc carnosine, artichoke leaf, ginger root, and DGL. These ingredients are well supported by evidence to heal the intestinal lining, encourage intestinal motility, and reduce upper digestive symptoms without interfering with normal digestive processes (7, 11).

Dose: one capsule twice daily

Duration: 8-12 weeks


A 2020 systematic review including 13 studies on GERD and probiotics concluded that supplemental probiotics ranging in dose from 1-46 billion CFU of various Lactobacillus and Bifidobacterium strains for up to 12 weeks significantly reduced symptoms of regurgitation, heartburn, nausea, and belching. It is important to note that probiotics, especially formulas containing prebiotic ingredients, often make patients with SIBO feel worse. If a patient reports worsening GERD symptoms after taking probiotics, discontinue and test for SIBO.

Dose: 4-10 billion CFU daily

Duration: 4-12 weeks

B Complex

Long-term use of PPIs is associated with vitamin B12 deficiency. Additionally, supplemental and dietary intake of vitamins B2, B6, and folate is associated with regression of GERD symptoms and a reduced risk of EE, BE, and esophageal cancer. (12-14)

Dose: one serving size (per label instructions) daily

Duration: at least one month; patients taking a concurrent PPI should continue until the PPI has been discontinued

When to Retest Labs

While it is common for patients to experience immediate improvement in symptoms, it often takes up to 12 weeks to resolve underlying factors, heal inflamed tissues, and observe complete regression of GERD symptoms. Longer protocols may be required depending on the chronicity of the disease and the severity of tissue damage. However, repeating labs three months after treatment initiation is reasonable to monitor treatment efficacy.



GERD is a common gastrointestinal condition of multifactorial origin, often related to lifestyle habits and lower esophageal sphincter dysfunction. Standard medical treatments focusing on symptom relief may be effective for some but are accompanied by a long list of potential side effects. Using various modalities, from dietary modifications to natural supplements, a root cause-based approach to GERD treatment can target and correct underlying imbalances predisposing to frequent reflux, heartburn, and GERD. A functional medicine provider can help in creating an effective GERD treatment protocol.

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


1. Locke, G.R. The Prevalence and Impact of Gastroesophageal Reflux Disease - About GERD. International Foundation for Gastrointestinal Disorders.

2. Greenan, S. (2022, January 7). 5 Lifestyle Habits That Increase Your Risk Of GERD. Rupa Health.

3. Sweetnich, J. (2023, February 17). Top 3 GERD Medications and Their Health Risk. Rupa Health.

4. Antunes, C., & Curtis, S.A. (2022, July 4). Gastroesophageal reflux disease. National Library of Medicine; StatPearls Publishing.

5. NIDDK. Barrett’s Esophagus. National Institute of Diabetes and Digestive and Kidney Diseases.

6. Rosen, R.D., & Winters, R. (2023, March 23). Physiology, Lower Esophageal Sphincter. PubMed; StatPearls Publishing.

7. Cloyd, J. (2023, February 21). A Functional Medicine GERD Protocol. Rupa Health.

8. Chen, C., Gong, X., Yang, X., et al. (2019). The roles of estrogen and estrogen receptors in gastrointestinal disease (Review). Oncology Letters, 18(6), 5673–5680.

9. Johns Hopkins Medicine. (2019, November 19). Pregnancy and Heartburn. Johns Hopkins Medicine.

10. Scott, M., & Gelhot, A.R. (1999). Gastroesophageal Reflux Disease: Diagnosis and Management. American Family Physician, 59(5), 1161–1169.

11. Sweetnich, J. (2023, February 21). Top Gut Healing Supplements Used By Integrative Medicine Practitioners. Rupa Health.

12. Sharp, L., Carsin, A., & Cantwell, M.M, et al. (2013). Intakes of Dietary Folate and Other B Vitamins Are Associated with Risks of Esophageal Adenocarcinoma, Barrett’s Esophagus, and Reflux Esophagitis. The Journal of Nutrition, 143(12), 1966–1973.

13. Pereira, Rde S. (2006). Regression of gastroesophageal reflux disease symptoms using dietary supplementation with melatonin, vitamins and amino acids: comparison with omeprazole. Journal of Pineal Research, 41(3), 195–200.

14. Lewis, J. R., Barre, D., Zhu, K., Ivey, K. L., Lim, E. M., Hughes, J., & Prince, R. L. (2014). Long-Term Proton Pump Inhibitor Therapy and Falls and Fractures in Elderly Women: A Prospective Cohort Study. Journal of Bone and Mineral Research, 29(11), 2489–2497.

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