Why and how to do an elimination diet—a reset for your gut

If you're experiencing unexplained bloating, fatigue, or digestive discomfort after meals, an elimination diet might be the diagnostic tool you need. Unlike restrictive fad diets, an elimination diet is a temporary, strategic approach to identifying which specific foods trigger your symptoms. For many of my patients at Dignity Integrative, this process becomes the foundation for lasting relief from chronic health issues that conventional medicine couldn't solve.

As just one case study, one of my patients came to me after visiting half a dozen specialists for her combination of joint pain, persistent fatigue, and digestive distress. Each specialist had focused on their particular domain—rheumatology prescribed anti-inflammatories, gastroenterology suggested managing IBS symptoms, endocrinology ran thyroid panels. But no one had looked at the whole picture or considered whether her daily food choices might be driving everything.

We started with a structured elimination diet. Within two weeks, her joint pain had diminished noticeably. By the end of the reintroduction phase, we'd identified gluten and dairy as clear triggers. What had seemed like separate, unrelated conditions turned out to be manifestations of food sensitivities that had been present for years.

We've written this guide based on the elimination diets we've successfully implemented with patients over the past three years. What follows is not theory—it's practical guidance drawn from real experience helping people identify food sensitivities that were undermining their health.

What Is An Elimination Diet?

An elimination diet is a systematic approach to identifying food sensitivities by temporarily removing common trigger foods from your diet, then carefully reintroducing them one at a time while monitoring your body's response. Unlike restrictive diets aimed at weight loss, an elimination diet is a diagnostic tool—a way to gather information about how your body reacts to specific foods.

The elimination diet protocol typically follows this pattern: you remove potentially problematic foods for two to four weeks, allowing your digestive system to calm and inflammation to decrease. Then comes the reintroduction phase, where you add foods back individually, watching carefully for reactions like bloating, skin changes, headaches, joint pain, or shifts in energy and mental clarity.

Dr. Albert Rowe first proposed this approach in 1926, and it remains one of the most reliable methods for identifying food sensitivities nearly a century later. Dr. Mark Hyman later popularized a ten-day version focused on reducing inflammation and optimizing gut health, though we often recommend longer elimination periods for patients with chronic conditions.

Who Should Consider an Elimination Diet

At Dignity Integrative, we typically have 90% of our patients complete this reset. This isn't because everyone has food sensitivities—it's because starting from a clean baseline gives us clarity. When patients begin their wellness journey with an elimination diet, we can see how their body functions without the noise of potential food triggers. It's like resetting your system before we build upon that foundation, layer by layer.

Having this base will provide a foundation that you can build upon, one layer at a time. The most common feedback that I have received is that it’s mind-clarifying, task-orienting, and easier to complete as the days go on.

But even if you aren’t involved with an integrative medicine practice like ours, an elimination diet can be a useful tool for anyone who is experiencing chronic health issues that may be related to food sensitivities.

This type of diet may be especially beneficial for individuals with autoimmune disorders, such as rheumatoid arthritis, lupus, or multiple sclerosis. These conditions are characterized by chronic inflammation in the body, and removing potential triggers from the diet may help reduce inflammation and improve symptoms.

Additionally, those with digestive problems like irritable bowel syndrome (IBS) or inflammatory bowel disease (IBD) may benefit from an elimination diet. These conditions can cause a variety of symptoms, including abdominal pain, bloating, gas, diarrhea, or constipation. Identifying and removing potential trigger foods may help reduce symptoms and improve overall digestive health.

Skin conditions like eczema, psoriasis, or acne may also be related to food sensitivities, and an elimination diet may help identify potential triggers. By removing common allergens and focusing on nutrient-dense, anti-inflammatory foods, individuals with skin issues may see an improvement in their symptoms.

Migraines are another condition that may be related to food sensitivities, and an elimination diet may be helpful for identifying potential triggers. Common trigger foods include dairy, gluten, chocolate, and caffeine. By removing these foods and slowly reintroducing them, individuals may be able to identify specific triggers and avoid them in the future.

Even if you don't have a specific chronic health issue, an elimination diet may be helpful if you're experiencing vague symptoms like bloating, fatigue, brain fog, or joint pain. These symptoms can be related to food sensitivities, and removing potential trigger foods may help improve overall health and well-being.

The Benefits of an Elimination Diet

The elimination diet can help with:

• Identifying food sensitivities: Pinpoint specific foods causing symptoms.

• Reducing inflammation: Remove potential trigger foods to support healing.

• Improving digestion: Reduce symptoms like bloating, gas, and diarrhea.

• Increasing energy levels: Remove problematic foods to boost energy.

• Enhancing mental clarity: Reduce brain fog and improve focus.

While I list all the wonderful benefits of this challenge, it is still a challenge! It takes self-discipline, strength, trust, and excitement to give your health the attention it deserves. Do not give up on yourself because your mind and your gut will thank you later!

Food Allergy vs. Food Intolerance

Food allergy is a reaction of the immune system to a specific food protein, while food intolerance is a non-immune reaction to a food component.

• Immune response: In food allergy, the immune system reacts to a specific food protein as if it were a threat, triggering an allergic reaction. In food intolerance, the immune system is not involved, and the reaction is caused by the body's inability to digest or process a certain food component.

• Severity of reaction: Food allergy reactions can range from mild to severe and can be life-threatening in some cases, while food intolerance reactions are generally less severe and do not pose a life-threatening risk.

• Timing of reaction: Food allergy reactions typically occur within minutes to a few hours of consuming the offending food, while food intolerance reactions may take longer to develop and may not be immediately obvious.

• Symptoms: Food allergy symptoms can include hives, swelling, difficulty breathing, and anaphylaxis, while food intolerance symptoms can include bloating, gas, diarrhea, and abdominal pain.

• Diagnostic tests: Food allergy can be diagnosed with skin prick tests or blood tests, while food intolerance may be diagnosed through elimination diets or other diagnostic tests, such as a lactose intolerance breath test.

Feature	Food Allergy	Food Intolerance
Immune response	Involves the immune system reacting to a food protein	Non-immune reaction to a food component
Severity of reaction	Can be life-threatening	Generally less severe
Timing of reaction	Typically occurs within minutes to a few hours of consuming the offending food	May take longer to develop
Symptoms	Hives, swelling, difficulty breathing, anaphylaxis	Bloating, gas, diarrhea, abdominal pain
Diagnostic tests	Skin prick tests, blood tests	Elimination diets, lactose intolerance breath test

It's important to note that food allergies and food intolerances can have similar symptoms, and it can be difficult to distinguish between the two without proper testing. If you suspect that you have a food allergy or intolerance, it's important to speak with a healthcare professional for proper diagnosis and treatment.

Why Elimination Diets Work When Testing Fails

Traditional allergy testing—skin pricks and IgE blood tests—only detect true food allergies, the kind involving immediate immune responses that can cause anaphylaxis. But food sensitivities operate differently. They involve delayed reactions, often mediated by IgG antibodies rather than IgE, and they trigger inflammation that can take hours or even days to manifest.

This is why a patient might get comprehensive allergy testing that comes back negative, yet still experience genuine symptoms from certain foods. The elimination diet captures what those tests miss. By removing foods and observing changes over weeks, then reintroducing them systematically, you're conducting a real-world experiment with your own body as both the laboratory and the control group.

Additionally, food sensitivities often involve the state of your gut lining. When you have increased intestinal permeability—what's commonly called leaky gut—larger food molecules can cross into your bloodstream, triggering immune responses. An elimination diet gives your gut time to heal while removing the triggers that caused the permeability in the first place. This is why patients often find they can reintroduce some foods successfully after several months of gut healing, even if those foods initially caused problems.

Getting Started

Preparing for the Elimination Diet

Before you begin an elimination diet, preparation matters more than you might think. Work with an integrative medicine physician or a registered dietitian who understands this approach—not just for accountability, but because proper guidance helps you avoid the pitfalls that can invalidate your results.

At Dignity Integrative, we pair every patient doing an elimination diet with our nutrition coach. Why? Because knowing which foods to eliminate is just the start. You need accountability, not to mention meal planning strategies, grocery shopping guidance, and someone to troubleshoot when you're standing in your kitchen at six o'clock wondering what you can actually eat for dinner. The patients who succeed are almost always the ones who have support.

Additionally, timing matters. Don't start an elimination diet the week before major holidays, during a stressful work deadline, or while traveling. Choose a period where you have some control over your environment and can dedicate mental energy to the process. There's never a perfect time, but there are certainly better and worse times.

Foods to Avoid During the Elimination Phase

During the elimination phase, you'll need to remove common allergens like gluten, dairy, soy, corn, eggs, and nuts. Additionally, you'll want to avoid processed foods, refined sugar, and artificial sweeteners.

Foods to Include During the Elimination Phase

Focus on eating whole, nutrient-dense foods like fruits, vegetables, lean proteins, and gluten-free grains like quinoa or brown rice. Incorporate anti-inflammatory foods like leafy greens, wild-caught fish, and turmeric to support healing.

Please refer to the chart below via Dr. Hyman's 10-Day Reset:

Category	Foods to Include	Foods to Avoid
Meats, poultry, and eggs	• Pasture-raised chicken, turkey, duck, pheasant • Pasture-raised and organic eggs • Grass-fed, pasture-raised lamb, beef, bison, venison, ostrich, deer, elk	​• Conventionally-raised chicken, duck, eggs, turkey • All processed meats and deli meats • Conventionally-raised bacon, beef, hot dogs, lamb, pork, sausage, salami
Fish and seafood	• Anchovies, clams, cod, crab, flounder, sole, herring, small halibut, mussels, wild salmon (canned or fresh), sardines, sable, shrimp, scallops, trout	• Larger fish like halibut, Chilean sea bass, tuna, swordfish
Nuts	• Almonds, Brazil nuts, cashews, hazelnuts, macadamias, pecans, pine nuts, pistachios, walnuts, raw cacao	• Peanuts • Nut butters that contain hydrogenated oils or sugar
Seeds	• Chia, flax, hemp, pumpkin, sesame, sunflower
Nut / Seed butters and flour	• Unsweetened almond, cashew, pecan, macadamia, walnut, coconut	• Peanut oil • Nut butters that contain hydrogenated oils or sugar
Oils	• Grass-fed ghee • Humanely raised tallow, lard, duck fat, chicken fat • Organic avocado oil, virgin coconut oil, almond oil, flax oil, hemp oil, macadamia oil, extra virgin olive oil, sesame seed oil, walnut oil, Tahini	• Canola oil, partially or fully-hydrogenated oils, margarine, peanut oil, soybean oil, sunflower oil, safflower oil, trans fats, vegetable oil, vegetable shortening
Vegetables	• Non starchy: organic artichokes, asparagus, avocado, bean sprouts, broccoli, Brussels sprouts, cabbage, cauliflower, celery, cucumber, eggplant, garlic, ginger root, kohlrabi, leafy greens, mushrooms, onions, peppers, radicchio, radish, rutabaga, seaweed, shallots, summer squash, tomatoes, turnips, zucchini • Starchy: yam, sweet potatoes, winter squash, pumpkin (limited to 1/2 cup per day)	• Corn, white potatoes
Dairy	• Grass-fed Ghee	• ALL dairy other than grass-fed ghee
Beans	• Green beans, green peas, gluten-free soy sauce, lentils, miso, tempeh, chickpeas, black beans, snap peas, snow pease	• Soy, soy milk, lima beans, baked beans • Avoid ALL beans if you have an autoimmune condition, pre-diabetes, diabetes, or leaky guy
Grains	• Quinoa (limited to 1/2 cup per day)	• Wheat, barley, rye, rice, amaranth, millet, spelt, oats, semolina couscous, all sources of gluten
Fruits	• Organic blackberries, blueberries, cranberries, kiwi, lemons, likes, raspberries (limited to 1/2 cup per day)	• High-glycemic fruits: bananas, dried fruit, fruit juice, grapes, mangoes, pineapples, apples, cherries, nectarines, peaches, pears, strawberries
Sugars and sweetners		• ALL sugars, sweeteners, and artificial sweeteners
Beverages	• Purified water, herbal tea, seltzer, mineral water	• Alcohol, coffee, soda, sugary beverages

How Long to Follow the Elimination Phase

During the elimination phase of the diet, it is important to strictly avoid the foods on the "Avoid" list and focus on consuming foods from the "Include" list.

The length of the elimination phase can vary depending on individual symptoms and goals. Generally, the elimination phase lasts between 2-4 weeks.

For some individuals, a longer elimination period may be necessary. This may be the case for those with severe or chronic health issues, who may require a longer period of time to allow the body to heal from inflammation and to fully eliminate the problematic foods from their system.

It is important to work with a healthcare professional or a registered dietitian to determine the appropriate length of the elimination phase based on individual needs and circumstances.

Once the elimination phase is complete, the reintroduction phase can begin. It's important to note that the elimination diet should not be followed indefinitely, as it can lead to nutrient deficiencies. Instead, it should be used as a tool to identify food sensitivities and to improve overall health and well-being.

Keeping a Food Diary to Track Progress

Keeping a food diary can help you track your progress during the elimination phase. Record what you eat, any symptoms you experience, and how you're feeling each day. This information can help you identify patterns and make adjustments as needed.

The Physiology of Elimination and Healing

Understanding what happens in your body during an elimination diet can help you stick with it when it feels difficult.

In the first few days, you might feel worse before you feel better. This isn't failure—it's actually a sign the process is working. When you remove foods your body has been reacting to, you can experience withdrawal-like symptoms: headaches, fatigue, irritability, or intensified cravings. This typically peaks around day three or four, then resolves.

By the end of the first week, most patients notice the first positive changes: more stable energy throughout the day, less bloating after meals, clearer thinking. Your gut lining is beginning to heal, inflammation is decreasing, and your immune system is calming down.

By weeks two through four, the changes become more pronounced. Chronic symptoms you'd accepted as normal—that persistent afternoon fatigue, the joint stiffness each morning, the skin issues that never quite cleared—often improve noticeably. This is your body in a less inflammatory state, and it's showing you what's possible.

This healing window is why we recommend at least two to four weeks for the elimination phase. Shorter periods don't give your body adequate time to demonstrate what it's capable of when it's not constantly fighting food-based triggers.

Reintroduction Phase

How to Reintroduce Foods

The reintroduction phase is a critical part of the elimination diet, as it allows you to identify which specific foods may be causing symptoms and which ones can be safely consumed without issue.

The process involves adding back one food group at a time, while carefully monitoring your body's reactions.

To begin the reintroduction phase, it is important to start with a small amount of the food being reintroduced. This allows you to gauge your body's response to the food without overwhelming your system. Begin with a small serving size, such as a quarter cup, and gradually increase over several days.

The systematic approach works like this: choose one food to reintroduce—let's say eggs. On day one, eat eggs for breakfast and lunch, then return to your elimination diet for the rest of that day and the following two days. During those three days, watch carefully for any reactions: changes in digestion, energy levels, sleep quality, joint pain, skin, or mood.

If you sail through those three days with no reactions, eggs are likely fine for you, and you can add them back permanently. Wait three clear days, then test the next food—perhaps dairy. This methodical pace feels slow, but it provides the clear data you need to build a sustainable eating plan based on your actual biology, not generic dietary advice."

Importance of Paying Attention to Your Body's Reactions

It's important to carefully monitor your body's reactions during this phase. Note any symptoms in your food diary that occur after consuming the reintroduced food.

Symptoms may include digestive issues, headaches, skin rashes, or joint pain. It is important to record the severity and duration of symptoms to accurately identify which foods are problematic.

If you don't experience any adverse reactions after reintroducing a specific food, you can continue to eat it as part of your regular diet. However, it is important to continue to consume the food in moderation and not overdo it, as excessive consumption of any food can lead to health issues over time.

Reintroducing Foods in a Systematic Manner

Reintroducing foods in a systematic manner is essential to accurately identifying food sensitivities. It is recommended to wait at least three days before reintroducing another food group, as this allows time for any potential symptoms to fully manifest.

The process of reintroducing foods can take several weeks or even months, depending on the number of food groups being tested and the severity of symptoms. However, the end result is a clearer understanding of which foods to avoid and which ones can be consumed without issue.

Foods to Reintroduce First

When reintroducing foods, it's important to start with the foods that are least likely to cause a reaction and gradually work your way up to more challenging foods. Here are some foods that are typically recommended to reintroduce first:

1. Non-gluten grains: This includes grains like rice, quinoa, and oats. These grains are generally well-tolerated and are less likely to cause reactions.

2. Legumes: Legumes, including beans, lentils, and chickpeas, are a good source of protein and fiber. However, some people may have difficulty digesting them, so it's important to reintroduce them slowly.

3. Dairy: Dairy products like milk, cheese, and yogurt are a common source of food sensitivity. It's important to choose high-quality dairy products and reintroduce them slowly to determine if your body can tolerate them.

4. Eggs: Eggs are a good source of protein and are included in many foods, so it's important to reintroduce them early in the process.

5. Gluten-containing grains: This includes grains like wheat, barley, and rye. Gluten is a common source of food sensitivity, so it's important to reintroduce these grains last and carefully monitor your body's reaction.

It's important to note that everyone's body is different, and what works for one person may not work for another. It's important to pay attention to your body's reactions and make adjustments accordingly. Additionally, if you have a known food allergy, it's important to avoid that food altogether, even during the reintroduction phase.

Tips for Success

Planning Meals During the Elimination Diet

Planning meals during the elimination diet can help ensure you're getting adequate nutrients and staying on track. Focus on simple, whole-food-based meals that incorporate a variety of nutrient-dense foods.

Read our post on meal-planning here.

Dealing with Cravings

Cravings can be a challenge during the elimination diet, but there are ways to cope. Incorporating healthy fats like avocado or nuts can help keep you feeling satisfied, while herbal teas or fruits like raspberries and blueberries can satisfy a sweet tooth.

Eating Out on an Elimination Diet

Eating out on an elimination diet can be challenging, but it's not impossible.

Research restaurants ahead of time and communicate your needs with the server. Many restaurants are accommodating to dietary restrictions, and you can always opt for simple dishes like grilled meat or fish with a side of vegetables.

Coping with Food Allergies and Sensitivities

Coping with food allergies and sensitivities can be overwhelming, but it's important to remember that you're not alone. Seek support from friends, family, or a qualified healthcare practitioner, such an integrative or functional medicine doctor.

Additionally, many online resources offer recipes, meal plans, and tips for navigating food allergies and intolerances.

Risks of an Elimination Diet

While an elimination diet can be a valuable tool for identifying food sensitivities and improving overall health, there are some potential risks and drawbacks to consider.

1. Nutrient Deficiencies: Eliminating entire food groups can lead to nutrient deficiencies if you are not careful to include a variety of nutrient-dense foods in your diet.

2. Social Isolation: Following a strict elimination diet can make social situations challenging and may lead to feelings of isolation or exclusion.

3. Disordered Eating: In some cases, the elimination diet can trigger disordered eating patterns or exacerbate an existing eating disorder.

4. Incomplete Results: While the elimination diet can be effective in identifying food sensitivities, it may not catch all of the underlying issues contributing to chronic health problems.

5. Difficulties with Compliance: Following a strict elimination diet can be challenging and may require significant planning, preparation, and discipline.

It's essential to consult with a healthcare professional before starting an elimination diet, especially if you have a history of disordered eating, nutrient deficiencies, or chronic health issues. A qualified healthcare provider can help you create a personalized plan that minimizes the risks and maximizes the benefits of the elimination diet.

FAQs

How is an elimination diet different from other diets?

Unlike weight-loss diets or lifestyle eating patterns like paleo or keto, an elimination diet is explicitly temporary and diagnostic. You're not eliminating foods because they're 'bad'—you're temporarily removing them to see if they're problematic for your specific body. Many elimination diets lead to weight loss as a side effect, but that's not the goal. The goal is information: which foods help you thrive, and which ones undermine your health?

How do I know if I have food sensitivities?

Symptoms of food sensitivities can vary, but common signs include bloating, gas, diarrhea, skin rashes, headaches, or joint pain. If you suspect you have a food sensitivity, consider an elimination diet or work with a qualified healthcare practitioner to identify potential culprits.

Can I do an elimination diet if I'm pregnant or breastfeeding?

It's important to consult with a qualified healthcare practitioner before starting an elimination diet if you're pregnant or breastfeeding. The elimination diet may not be appropriate for everyone, and it's essential to ensure you're getting adequate nutrients for you and your baby.

Is an elimination diet safe for children?

An elimination diet may be appropriate for children with chronic health issues or suspected food sensitivities, but it's important to work with a qualified healthcare practitioner to ensure adequate nutrient intake. Additionally, it's important to ensure children are getting enough calories for growth and development.

Can an elimination diet cure food allergies?

An elimination diet cannot cure food allergies, but it can help identify potential triggers and reduce inflammation in the body. If you have a food allergy, it's essential to avoid that food entirely and carry appropriate medications like an EpiPen in case of accidental exposure.

How long should I wait between reintroducing foods?

It's recommended to wait 2-3 days between reintroducing foods to allow enough time for any potential reactions to manifest. Additionally, it's important to ensure you're feeling well before adding in another food group.