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5 Functional Medicine Lab Tests That Can Be Run During the GAPS Diet Protocol to Customize Nutritional Needs for Your Patients

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5 Functional Medicine Lab Tests That Can Be Run During the GAPS Diet Protocol to Customize Nutritional Needs for Your Patients

The GAPS diet theory states that eliminating certain foods from the diet can help people treat various conditions that affect the whole body. The concept of leaky gut is becoming increasingly recognized. Advances in science and research continue to support the importance of an intact intestinal barrier and a balanced intestinal microbiome for systemic health and wellness. This article will discuss the GAPS diet and how it can be successfully implemented in clinical practice.


What Is the GAPS Diet?

The GAPS (Gut and Psychology Syndrome) diet is a nutritional protocol developed by Dr. Natasha Campbell-McBride. Adapted from the Specific Carbohydrate Diet (SCD) principles and understanding that physical and mental health conditions stem from gut imbalances, the GAPS diet focuses on healing and restoring gut health and function.

The GAPS diet is a multi-phased dietary plan that emphasizes eliminating certain foods; incorporating homemade broths, probiotic-rich foods, easily digestible foods, and healthy fats; and the gradual reintroduction of foods back into the diet. The diet guidelines also encourage stress reduction techniques and physical activity to support overall health. (6)

Who Could Benefit From the GAPS Diet?

Dr. Campbell-McBride formulated the GAPS diet based on the premise that a leaky gut (a compromised gut lining) allows undigested food particles, toxins, and other foreign substances into the bloodstream, leading to systemic inflammation and psychological, neurological, and behavioral issues. The diet was originally designed for patients with neurocognitive and mental health disorders, including autism spectrum disorder, attention deficit hyperactivity disorder (ADHD), dyslexia, depression, anxiety, epilepsy, obsessive-compulsive disorder (OCD), bipolar disorder, and schizophrenia. (6)

However, because the diet strongly emphasizes dietary modifications specific to reducing intestinal and systemic inflammation, improving digestion, and improving the integrity of the gut barrier, patients suffering from other conditions stemming from gut-related imbalances and dysfunction can benefit from the diet. The GAPS diet may be indicated for those with food sensitivities and allergies, small intestinal bacterial overgrowth (SIBO), celiac disease, inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), eczema, asthma, or autoimmune disease. (6)

The GAPS diet may not be necessary or suitable for everyone. Before beginning any diet, speaking with a qualified healthcare professional experienced with the GAPS diet is important.

What Is the GAPS Diet Protocol?

The GAPS diet protocol takes an individual through three stages, each with its own instructions for dietary modifications.

Introduction Stage

Dr. Campbell-McBride recommends that most people follow the Introduction Diet before starting the Full GAPS diet. This initial stage is the most restrictive part of the GAPS diet and typically lasts for a few weeks to several months, although it can last up to a year, depending on individual needs and symptoms. The introduction diet takes the patient through six progressive steps that the person proceeds through as their digestive symptoms improve.

The following foods are eliminated from the diet at the beginning (Stage 1) of the introduction diet (1):

  • Grains: wheat, rice, corn, oats, barley, rye, quinoa, and amaranth
  • Starchy Vegetables (e.g., potatoes, sweet potatoes, parsnips)
  • Refined Sugars: table sugar, high-fructose corn syrup, artificial sweeteners, candies, desserts
  • Processed Foods: processed meats, packaged snacks, fast food
  • Dairy Products (except for ghee and clarified butter): milk, cheese, yogurt, ice cream
  • Legumes: beans, lentils, soybeans
  • Nuts and Seeds rich in omega-6 fatty acids: peanuts, cashews, pistachios, sesame seeds, sunflower seeds

Stage 1

The foods to be eaten during Stage 1 include those listed below. These are the foundational food items from which the GAPS Diet is built. (1)

  • Homemade meat stock/broth
  • Boiled meat or fish
  • Homemade soups with broth, meat, and well-cooked vegetables; start with carrots, zucchini, squash, mushrooms, onions, bell peppers, broccoli, cauliflower
  • Probiotic foods: fermented vegetable juice, yogurt, or kefir (if dairy is tolerated)
  • Ginger or chamomile tea with raw honey
  • Purified water

Stage 2

In Stage 2, the patient adds the following foods into their diet (1):

  • Organic egg yolks
  • Casseroles and stews made with meats and vegetables
  • Fermented fish
  • Homemade ghee

Stage 3

In Stage 3, the patient adds the following foods into their diet (1):

  • Ripe avocado
  • Three-ingredient pancakes made from organic nut butter; eggs; and a fresh piece of winter squash, marrow, or zucchini
  • Scrambled eggs
  • Sauerkraut and fermented vegetables

Stage 4

In Stage 4, the patient adds the following foods into their diet (1):

  • Roasted and grilled meats
  • Cold-pressed olive oil
  • Freshly pressed carrot juice
  • Homemade bread made from nut flour; eggs; natural fat; fresh winter squash, marrow, or zucchini; and salt to taste

Stage 5

In Stage 5, the patient adds the following foods into their diet (1):

  • Cooked apple puree
  • Raw vegetables
  • Fresh-pressed juices
  • Raw vegetables: start with lettuce and peeled cucumber, and gradually add more diversity as tolerated

Stage 6

In Stage 6, the patient adds the following foods into their diet (1):

  • Raw, peeled apple
  • Raw fruit
  • Increase honey
  • Homemade baked goods sweetened with dried fruit

Dairy Introduction

The dairy introduction is designed for patients who skip the introduction diet or eliminate dairy while going through it due to a known sensitivity to dairy. Dr. Campbell-McBride recommends the following steps for an elimination-rechallenge of dairy:

  • Step 1: Avoid all dairy for 4-6 weeks
  • Step 2: Introduce homemade ghee from raw organic butter
  • Step 3: Introduce raw organic cultured butter
  • Step 4: Introduce homemade yogurt and sour cream made from raw, organic milk and cream using yogurt culture
  • Step 5: Introduce homemade kefir and sour cream made from raw, organic milk and cream using kefir culture
  • Step 6: Introduce homemade cottage cheese
  • Step 7: Introduce commercially available, organic cheeses

Full GAPS Diet

The Full GAPS diet builds off the essential concepts of the Introduction Stage (homemade broths, soups, and probiotics foods), while expanding the variety of foods the patient can incorporate into their diet. Most patients will follow this diet for 1.5-2 years. Processed foods, grains, starchy vegetables, refined sugars, and most dairy products are still excluded from the diet. The Full GAPS diet emphasizes wholesome foods, including quality proteins, healthy fats, non-starchy vegetables, fermented foods, and probiotics. A complete list of acceptable GAPS foods and those to be avoided can be found here.

Reintroduction Phase

After experiencing at least six months of normal digestion, people can move on to the Reintroduction Phase of the GAPS diet. This final stage involves gradually reintroducing more food items into the diet over several months. Each food is introduced one at a time, with a waiting period of a few days before introducing another, to allow time to identify food sensitivities or intolerances. Dr. Campbell-McBride recommends starting with potatoes and fermented grains and continuing with starchy vegetables, grains, and beans. (2)

The patient should maintain a healthy, nutrient-dense diet while avoiding problematic foods. The Reintroduction Phase allows for an individualized approach to a diet based on personal preference and tolerance. (2)

What Are the Supplements Used With the GAPS Diet?

Certain dietary supplements can complement the GAPS diet’s nutritional changes and provide additional nutritional or anti-inflammatory benefits. Dietary supplements should be chosen based on the patient’s needs and introduced into the GAPS protocol once a patient’s diarrhea and other serious digestive symptoms have cleared. It is important to consult a healthcare provider before starting any new supplements and choose medical-grade, third-party tested products that follow Good Manufacturing Practices. (3, 4)


Probiotic supplements contain beneficial bacteria that help restore a healthy balance of gut flora and improve digestion. Finding a therapeutic-dose, broad-spectrum probiotic containing spore-based bacteria and a range of Lactobacillus and Bifidobacterium strains is recommended. (3)

Cod Liver Oil

Dr. Campbell-McBride recommends cod liver oil as a rich source of EPA and DHA fatty acids and vitamins A, D, E, and K (3). Cod liver oil provides anti-inflammatory benefits and supports the body’s natural immune and detoxification systems.

Essential Fatty Acids

Omega-3 essential fatty acids (EPA and DHA) are not naturally produced by the body and, therefore, need to come from the diet. They have potent anti-inflammatory properties that support brain health, cardiovascular function, and overall well-being.

Digestive Enzymes

Digestive enzymes support the breakdown of food, improve nutrient absorption, and reduce digestive discomfort related to mealtimes. A broad-spectrum digestive enzyme will contain enzymes to support the proper digestion of proteins, carbohydrates, and fats. (5)

Vitamins and Minerals

Depending on individual health concerns and known nutrient deficiencies, targeted nutrient support may be required. This may include, but is not limited to, choline, vitamin C, alpha lipoic acid, and magnesium. (3)

What Does the Evidence Say?

A lack of well-designed clinical trials and large-scale studies assessing the GAPS diet exists. Most of the available evidence consists of case studies, anecdotal reports, and theoretical frameworks proposed by Dr. Campbell-McBride.

However, the understanding of gut health, the microbiome, and its influence on whole-body health is rapidly evolving. Current research strongly supports the model of the gut-brain axis, a dynamic bi-directional relationship between the gastrointestinal system and the brain. Altered gut microbiota compositions have been noted in those with various mental health conditions, including major depressive disorder, generalized anxiety disorder, OCD, bipolar disorder, schizophrenia, and addiction.

Further research also supports the importance of gut health concerning other health conditions Dr. Campbell-McBride claims can be treated with the GAPS diet, including autoimmune diseases, skin health, fibromyalgia, asthma, and gastrointestinal diseases.

Functional Medicine Labs That Can Be Run During the GAPS Diet Protocol to Customize Nutritional Needs

Functional medicine tests help functional providers personalize treatment options for their patients interested in or following the GAPS diet protocol. Below are some labs that could be considered to help patients meet their health goals with the GAPS diet.

Organic Acids

An organic acids test (OAT) is a great metabolic screening tool, often recommended by functional providers for patients with autism and gastrointestinal disorders. This urinary test measures metabolic byproducts excreted from the body through the kidneys that can give valuable information regarding systemic and neurologic inflammation, intestinal dysbiosis, essential nutrient status, energy production, and neurotransmitter metabolism.

Gastrointestinal Assessment

A comprehensive gastrointestinal assessment can help quantify intestinal permeability and identify its underlying causes. Helpful testing options include an intestinal permeability test, a comprehensive stool analysis, and a SIBO breath test.

Nutritional Assessment

A micronutrient panel measures the levels of important vitamins, minerals, antioxidants, fatty acids, and amino acids. This test helps tailor recommendations regarding specific foods and supplements that should be emphasized during the GAPS protocol.

Food Sensitivities

While the GAPS diet lays out strict guidelines on foods to eat and avoid during each stage, this should always be modified to the patient’s food sensitivities and intolerances. A food sensitivity test helps take the guesswork out of elimination diets and can be an exceptionally beneficial tool in customizing dietary modifications.



The GAPS diet is a multiphased restrictive elimination diet that removes grains, pasteurized dairy, starchy vegetables, and refined carbohydrates to heal the gut, reduce inflammation, and treat various health conditions. While the GAPS diet has gained attention and popularity among individuals and practitioners, the scientific evidence supporting its effectiveness is currently limited. More research is needed to better understand its potential benefits and impact on various health conditions. However, based on its proposed mechanism of action- the concept of leaky gut and its impact on physical and mental health- it’s reasonable to think that many could benefit from following the protocol. What works for one person may not work for another, and the GAPS diet may not be suitable or necessary for everyone. A knowledgeable healthcare provider can provide personalized guidance on completing the GAPS diet based on individual needs and medical history.

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. Campbell-McBride, N. Introduction Diet. Retrieved June 15, 2023, from

2. Eske, J. (2019, April 26). GAPS diet: What it is, uses, effectiveness, and food guide.

3. Supplement Guide. GAPS Diet. Retrieved June 15, 2023, from

4. Introduction Diet. GAPS Diet.

5. Cloyd, J. (2023, May 24). What are Digestive Enzymes: How to Test Your Patients Levels. Rupa Health.

6. About - GAPS Diet. GAPS Diet.

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