Living Well & Understanding the Body:

Elimination Diets: What You Need to Know

Margaux Thieme-Burdette January 13, 2022

With food sensitivities and intolerances impacting 15-20% of the population (1), many people—especially in the autoimmune disease and chronic illness communities—are turning to food to uncover issues and feel better. When used mindfully and appropriately, elimination diets can be powerful healing tools; however, there are some precautions to take. Read on for the risks and benefits, as well as five common diets.

What Are Elimination Diets?

Elimination diets are tools to identify food sensitivities and intolerances, as well as to reduce symptoms like brain fog, joint pain, rashes, anxiety, bloating, and fatigue.

These diets, a.k.a. exclusion or healing diets, involve temporarily excluding foods that may be problematic and trigger symptoms. This is called the elimination phase of the protocol, which can last anywhere from two to six weeks on average. Next, foods are challenged one-by-one to see how the body reacts. If a food does not trigger symptoms, it may be reintroduced back into the diet.

Depending on the body’s reactions as well as the specific protocol being followed, certain foods may remain out of the diet for a long period of time. Foods that are not currently tolerated can sometimes be incorporated back into the diet after the body has had an opportunity to heal. In elimination diets, the foods most commonly excluded are dairy, gluten, sugar, nightshades, soy, alcohol, and processed foods.

Elimination diets are becoming more popular as doctors are using them to identify and treat patients. Studies have shown that elimination diets can reduce symptoms in individuals with irritable bowel syndrome (2), eosinophilic esophagitis (3, 4, 5), eczema (6, 7), and autoimmune diseases like Crohn’s disease and ulcerative colitis (8), as well as Hashimoto’s thyroiditis (9).

People use elimination diets when they:

  • Want to feel better and are looking for more natural approaches
  • Cannot tell which (or if) foods are triggering their symptoms
  • Are stuck in their health journeys and do not know what to do next
  • Feel they have exhausted all options and their doctors are unable to help
  • Have particularly stubborn health issues that have not improved after addressing known root causes

How Do They Work?

There are many types of elimination diets out there. The protocol you use will depend on your symptoms and health condition. Each elimination diet has its own instructions regarding “yes” and “no” foods, what to challenge first and how, and when to reintroduce. However, they all follow a similar method: eliminate, challenge, and reintroduce. Use a journal to keep track of the way you feel throughout each phase, especially while challenging foods.


Avoid eating foods on the “no” list for a short period, typically three to six weeks. Pay attention to labels, as well as extracts or derivatives of your “no” foods. If you happen to eat an excluded food, you may need to rewind and start the protocol from the beginning. Notice whether your symptoms have improved, stayed the same, or gotten worse, and keep in touch with your practitioner about how you’re feeling. If symptoms have not improved, you may need to remain in the elimination phase for a longer amount of time.


Try eating your excluded foods one at a time, noticing any reactions. Write down the date, time, symptoms, and amount of food. Use singular foods, like fresh corn kernels, rather than products with the food mixed in, like cornbread. You may choose to separately challenge different varieties or preparations of the same food, such as almonds and almond milk. Wait three to seven days between food challenges and start with a small amount of food, increasing the amount daily. The exact methods will vary depending on the protocol and the practitioner who is guiding you.


You may reintroduce foods as you challenge them, or wait until all foods have been tested before you include any of them back in your diet. Continue paying attention to how you feel. You may find that your body tolerates eggs, for example, but only one or two per week. This can shift over time. Work with your practitioner to develop a personalized eating plan.

→ Check out The Elimination Diet, an in-depth resource from the University of Wisconsin-Madison School of Medicine and Public Health

5 Common Elimination Diets

  • Low-FODMAP: remove or limit foods high in FODMAPs (fermentable oligo-, di-, and monosaccharides and polyols), “a group of sugars that are not completely digested or absorbed in our intestines” (10). Often used to treat IBS or SIBO. Resources: Monash University (and FODMAP Diet App)
  • Autoimmune Protocol (AIP): remove potentially inflammatory and immune-stimulating foods while increasing nutrient-dense foods to manage and treat autoimmune diseases. AIP emphasizes other lifestyle factors in addition to diet. Resources: Autoimmune Wellness, Dr. Sarah Ballantyne
  • Gut and Psychology/Physiology Syndrome (GAPS): remove foods that are difficult to digest, while incorporating nutritious whole foods in order to treat neurological and psychological conditions. Resources:, Gut and Psychology Syndrome (book)
  • Specific Carbohydrate Diet (SCD): remove grains as well as foods containing sugars called di- and polysaccharides, while adding nutritious whole foods to help balance the gut microbiome. Often used to treat ulcerative colitis, Crohn’s disease, and IBS. Resources: Medical News Today, Breaking the Vicious Cycle: Intestinal Health Through Diet (book)
  • Whole30: remove potentially inflammatory and problematic foods such as grains, sugar, alcohol, and dairy. Resources: Whole 30 Program

Apart from the above well-known protocols, there are countless other options and ways to complete an elimination diet. Many doctors, dieticians, medical clinics, and health educators design their own plans that they use with patients or promote online. You may also focus on one food or or food group, such as dairy. Note that eating plans like the ketogenic and paleo diets are not commonly used as elimination diets, but can be. With the endless options available, it is especially helpful to work with a professional who understands your unique needs.

Potential Benefits & Risks of Elimination Diets


  • Reduce and manage symptoms (2-9)
  • Discover food triggers
  • Decrease inflammation (8)
  • Learn how to listen to your body
  • Take control of your health
  • Create a personalized eating plan


  • Rely too heavily on the diet to feel better
  • Remain in the elimination phase too long
  • Unintentionally decrease diversity and nutrients
  • Ignore other underlying issues and root causes
  • Develop disordered eating patterns

What to Consider Before Starting

1. Is this the right time to take on a food-focused lifestyle change?

2. Is an elimination diet the best way to address your health concerns?

3. Do you have a personal or family history of eating disorders?

4. What kind of medical and personal support do you have available?

5. Have you been able to investigate and address underlying issues with your healthcare providers, such vitamin and mineral deficiencies?

6. How much time and energy will you need to complete the protocol?

The Bottom Line

Elimination diets temporarily remove foods that tend to be inflammatory, immune-stimulating, or difficult to digest. After a period of time, foods are challenged in order to detect sensitivities and intolerances. When used as short-term nutritional tools, they can improve quality of life and be an invaluable part of the healing journey for people with autoimmune disease, IBS, and other health conditions. However, elimination diets may not be the best approach for everyone—particularly for those with a history of eating disorders or disordered eating. Know yourself, talk with your healthcare team, and follow the path that feels right for you.


  1. Article Sources and Footnotes
    1. Lomer M. C. (2015). Review article: the aetiology, diagnosis, mechanisms and clinical evidence for food intolerance. Alimentary pharmacology & therapeutics, 41(3), 262–275.

    2. Atkinson, W., Sheldon, T. A., Shaath, N., & Whorwell, P. J. (2004). Food elimination based on IgG antibodies in irritable bowel syndrome: a randomised controlled trial. Gut, 53(10), 1459–1464.

    3. Syrigou, E., Angelakopoulou, A., Zande, M., Panagiotou, I., Roma, E., & Pitsios, C. (2015). Allergy-test-driven elimination diet is useful in children with eosinophilic esophagitis, regardless of the severity of symptoms. Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology, 26(4), 323–329.

    4. Vashi, R., & Hirano, I. (2013). Diet therapy for eosinophilic esophagitis: when, why and how. Current opinion in gastroenterology, 29(4), 407–415.

    5. Spergel, J. M., Andrews, T., Brown-Whitehorn, T. F., Beausoleil, J. L., & Liacouras, C. A. (2005). Treatment of eosinophilic esophagitis with specific food elimination diet directed by a combination of skin prick and patch tests. Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology, 95(4), 336–343.

    6. Dhar, S., & Srinivas, S. M. (2016). Food Allergy in Atopic Dermatitis. Indian journal of dermatology, 61(6), 645–648.

    7. Pacor, M. L., Peroli, P., Nicolis, F., Bambara, L. M., Givanni, S., Marrocchella, R., & Lunardi, C. (1990). Eczema e allergia alimentare nell’adulto [Eczema and food allergy in the adult]. Recenti progressi in medicina, 81(3), 139–141

    8. Konijeti, G. G., Kim, N., Lewis, J. D., Groven, S., Chandrasekaran, A., Grandhe, S., Diamant, C., Singh, E., Oliveira, G., Wang, X., Molparia, B., & Torkamani, A. (2017). Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease. Inflammatory bowel diseases, 23(11), 2054–2060.

    9. Abbott R D, Sadowski A, Alt A G (2019) Efficacy of the Autoimmune Protocol Diet as Part of a Multi-disciplinary, Supported Lifestyle Intervention for Hashimoto’s Thyroiditis. Cureus, 11(4): e4556. doi:10.7759/cureus.4556

    10. FODMAPs and Irritable Bowel Syndrome. (n.d.) Monash University

    11. UW Integrative Health. (n.d.) The Elimination Diet. University of Wisconsin, Madison, School of Medicine and Public Health

    12. Heal the Gut with the IFM Elimination Diet. (n.d.) The Institute for Functional Medicine

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