Your 3-Step Guide to an Effective Elimination Diet

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Your 3-Step Guide to an Effective Elimination Diet

A Short-Term Elimination Diet Can Lead to More Long-Term Food Freedom

Key Takeaways:

  • An elimination diet is an effective 3-step process to identify the food sensitivities and intolerances that may be impacting your gut and general health.
  • You start by eliminating potential trigger foods for 3–4 weeks. 
  • Trying the least restrictive elimination diet option first is best—a Paleo or low-FODMAP framework works for most people.
  • The second step is the reintroduction phase, when you discover which foods are causing problems.
  • The third step is maintenance, when you move forward with a balanced diet while taking care of your sensitivities.
  • As your microbiome gets healthier and your immune reactivity calms, you may be able to tolerate foods that previously triggered symptoms.

An elimination diet is a three-step process that helps you identify the food sensitivities and intolerances that could be impacting your gut and wider health.

Done right, an elimination diet ​​isn’t particularly complicated. But you do need to avoid some common pitfalls that can make the process harder or less successful than it could be.

There’s a wide variety of at-home blood and hair analysis tests that claim to make easier work of identifying food sensitivities, but they are rarely (if ever) accurate and thus not advised [1, 2, 3]. Though it is a little more involved, an elimination diet is the gold standard for identifying foods you don’t tolerate well.

In this article, I’ll break down the three distinct stages of an elimination diet and how to make these as trouble-free as possible. The steps are elimination, reintroduction, and maintenance. 

But before getting into all that, let’s take a look at why elimination diets are necessary in the first place. This requires an understanding of what food sensitivities are and how they can undermine your gut and overall health. 

What are Food Sensitivities and Intolerances?

You will often find the terms food sensitivity and food intolerance used interchangeably, as there is no officially recognized distinction between the two. The symptoms of each can vary and overlap, making it hard to identify the best category for a food reaction.

However, it is becoming more common for gut health-focused practitioners to categorize food sensitivity and food intolerance separately, as follows:

Food intolerance refers to an impaired ability to process or digest certain food components. For example, with lactose intolerance, you lack the lactase enzyme needed to break down the lactose in dairy products. As a result, eating dairy can cause gas, bloating, gut pain, and nausea. 

With histamine intolerance, symptoms typically arise when you lack an enzyme called diamine oxidase that breaks down histamine. Eating high-histamine foods when you are histamine intolerant can cause allergy-like symptoms such as itchy skin, along with headaches, fatigue, and immune responses in your gut and elsewhere [4, 5, 6, 7].

Reacting to too many of certain carbohydrates (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols, or FODMAPs), is also a type of food intolerance. Typical symptoms are abdominal pain, gas, and bloating [8, 9].

Symptoms of food intolerance tend to show up within minutes to hours of eating an offending food.

Food sensitivity, on the other hand, is a more general food reactivity that involves inflammation, abnormal immune reactions, and microbiome changes. Food sensitivity symptoms tend to show up hours or days after eating something and may include fatigue, headaches, joint pain, and brain fog.

Perhaps the most common example of a food sensitivity is non-celiac gluten sensitivity. While it’s still frequently referred to as gluten intolerance, gluten sensitivity is the more accurate way to refer to this condition [10]. 

That said, try not to get too hung up about what’s a food intolerance versus a sensitivity. The distinctions aren’t set in stone, and there is a lot of potential for crossover. 

For example, many people who believe they need a gluten-free diet may actually be intolerant to other components of wheat, such as fructans, which are a type of FODMAP [11, 12, 13].

Food Allergies and Celiac Disease Are Different

Food allergy is distinct from food sensitivity and food intolerance. In a classic food allergy, the immune system sees common food proteins as invaders and produces immunoglobulin E (IgE) antibodies against them in defense. When those proteins enter the body, the immune system mounts a reaction, which causes symptoms that can range from mild (like a rash) to life-threatening medical emergencies. Worst case scenario, allergies to foods such as peanuts or shellfish can cause anaphylactic shock, in which your blood pressure drops suddenly and your airways narrow, so you can’t breathe [14].

Food intolerance and sensitivity are also distinct from celiac disease, which is an autoimmune condition. In celiac disease, the immune system attacks its own tissues when you eat gluten. 

With most food intolerances and sensitivities, you may be able to cope with a little of the trigger food before symptoms develop. This is not the case with celiac disease or a full-blown allergic reaction to food, which require full avoidance of the food.

In this article, the elimination diet steps I’ll describe are designed to help you identify and deal with food intolerances and sensitivities—not food allergies or celiac disease. 

Two literature reviews concluded that an elimination diet is the most useful diagnostic test for suspected food intolerances, including FODMAPs, wheat, and histamine [15, 16]. Another review found the same is true for non-celiac gluten sensitivity [17]. 

In contrast, to diagnose suspected food allergies, you’ll need a medically supervised skin-prick test, allergy blood tests, and possible elimination diets with food challenges. If you’ve had anaphylaxis, doctors can use the event to diagnose an allergy after the fact. Identifying celiac disease also requires a blood test and possibly a biopsy of your small intestine.

Ultimately, most types of food sensitivity and intolerance will directly or indirectly result in inflammation, an unbalanced gut microbiota, and abnormal immune reactions. This means that even though the root causes may differ, the solution—a well-constructed elimination diet—is the same.

Let’s now look at the first step in your elimination diet plan—the elimination phase itself.

Step One: Eliminating Potential Trigger Foods

Before you begin eliminating foods, it’s a good idea to make sure you are starting with a basis of primarily whole, fresh foods. This is because added sugars, trans fats, artificial sweeteners, and refined-carbohydrate foods (like cookies and chips) can cause gut symptoms, complicating the picture when you are trying to figure out which foods may be problematic for you.

Numerous choices exist for structuring your healthy elimination diet meal plan, with the most common diets we use in the clinic being Paleo, low-FODMAP, and the autoimmune protocol (AIP). Sometimes patients prefer an elemental diet.

A common mistake is that people start out with a diet that is far more restrictive than they may need, and they struggle to stick to it. This is why we typically introduce individuals to the Paleo diet at first. It eliminates common food triggers for sensitivity or intolerance while being less restrictive than the other two elimination diets. 

The Paleo Diet

Unless you have a specific reason to start with another diet first, I recommend that you begin with this elimination diet. The Paleo diet is based roughly on what our Paleolithic ancestors likely ate, before the agricultural revolution. Compared with the modern Western diet, the Paleo diet counts as an elimination diet because it cuts out grains, legumes, dairy, processed fats and oils, and artificial additives and sweeteners.

Here is a breakdown of foods you’ll cut out on a Paleo elimination diet, and those you can eat instead. 

Foods to Eliminate Foods to Eat Instead
Grains and legumes, such as all types of bread, pasta, cereals, rice, peas, beans, peanuts, and chickpeasExtra vegetables (see below); nuts and seeds other than peanuts
Potatoes Non-starchy veggies, such as cauliflower, broccoli, Brussels sprouts, artichokes, asparagus, and carrots. Sweet potatoes are ok in moderation.
Refined vegetable oils, such as corn, peanut, and canola oilHealthy fat sources like avocados, avocado oil, extra virgin olive oil, and coconut oil 
Milk and other dairy productsAlmond or cashew milk, ideally homemade with just nuts and water 
High-sugar fruits like mangoes, grapes, bananas, pears, and apples (reduce rather than remove)Strawberries, raspberries, blackberries, and blueberries (the lowest-carbohydrate fruits) 
Highly processed meat and fish products like hot dogs, chicken tenders, and deli meatsSimple cuts of fresh meat and fish, grass-fed and wild-caught where possible; pasture-raised eggs 
Processed foods and beverages, artificial sweeteners, and additives in generalSimple home-cooked meals; water, and herbal teas to drink

It’s also a good idea to temporarily remove all sources of caffeine, like tea and coffee, when you’re doing any type of elimination diet. But if you regularly drink caffeine, do this slowly by reducing your intake a little each day, replacing full-caf with half- or quarter-caf coffee, and drink more water for at least a week to reduce your withdrawal symptoms.

In just a few weeks, a Paleo diet can help decrease inflammation by removing foods that cause an immune response [18]. This is probably why many of my patients report significant symptom improvement within a few weeks of adopting the Paleo diet.

However, if after 3–4 weeks you are still getting symptoms such as bloating, stomach pain, fatigue, and brain fog, it’s possible you haven’t eliminated all the foods that might be triggering your symptoms. Particularly if you still have a lot of bloating and other symptoms that might be related to an irritable bowel, a more suitable elimination diet for you could be a low-FODMAP diet.

A Low-FODMAP Diet

The Paleo diet removes some FODMAPs, such as beans and wheat, but it doesn’t remove others, like broccoli, Brussels sprouts, pears, and onions. A low-FODMAP diet is therefore the next logical step if your food sensitivity symptoms still remain after a few weeks on a Paleo diet.

FODMAPs are fermentable carbohydrates that the small intestine can’t completely digest or absorb and which attract water into the gut as they pass through. When FODMAPs reach the bowel (large intestine), the gut bacteria there ferment them and produce a lot of gas in the process. The surplus gas and water associated with FODMAPs cause the intestinal wall to stretch and expand, which can create significant pain and discomfort for those with heightened gut sensitivity [19].

An exclusion diet based on a low-FODMAP framework may be particularly relevant for you if you have irritable bowel syndrome (IBS), or small intestinal bacterial overgrowth (SIBO), which often co-occur. This is logical when you think about it because when you already have bacterial overgrowth, feeding gut bacteria with fermentable carbs like FODMAPs will just make them multiply more. The result? More abdominal pain and bloating.

Below is a list of the high-FODMAP foods to avoid, and the lower-FODMAP ones you can have in their place. Scientists at Monash University in Melbourne, Australia, have done most of the in-depth work on the low-FODMAP diet, and this table is based on their work. You can also download this useful app from Monash, which will help you to navigate the various stages of a low-FODMAP diet more easily and eat the most varied diet possible.

Food GroupHigh-FODMAP (eliminate)Low-FODMAP (include)
VegetablesArtichoke, asparagus, cauliflower, garlic, green peas, mushrooms, onions, sugar snap peasAubergine/eggplant, green beans, bok choy, green bell pepper, carrot, cucumber, lettuce, potato (ok in moderation)
FruitApples, apple juice, cherries, dried fruit, mangos, nectarines, peaches, pears, plums, watermelonCantaloupe, kiwifruit, mandarin, orange, pineapple, blueberry
DairyCow’s milk, custard, evaporated milk, ice cream, soy milk (made from whole soybeans), sweetened condensed milk, yogurtAlmond milk, brie/camembert cheese, feta cheese, hard cheeses, lactose-free milk, soy milk (if you aren’t sensitive to soy protein)
LegumesMost legumes, Firm tofu, mung beans, peanuts
Meat, seafood, and eggsSome marinated meats/poultry/seafood and processed meats with additivesPlain-cooked fresh meats/poultry/seafood, and eggs; prepared meats without additives
Grain foodsWheat/rye/barley-based breads and breakfast cerealsPlain oats, quinoa flakes, quinoa/rice/corn pasta, rice cakes, sourdough spelt bread, wheat/rye/ barley-free breads
SweetenersHigh-fructose corn syrup, honey, sugar-free confectionsDark chocolate, maple syrup, rice-malt syrup, table sugar (all in moderation only)
Nuts and seedsCashews, pistachiosMacadamias, peanuts (which are legumes), pumpkin seeds, walnuts

Most people who eliminate high-FODMAP foods from their diet get good results, especially if they have IBS symptoms like abdominal pain, bloating, constipation, diarrhea, and flatulence [20].

However, if you still have nagging symptoms, especially non-digestive ones like fatigue, skin problems, or brain fog, you may need to pivot again. Other elimination diets you can try are the AIP diet and the low-histamine diet.

More Restrictive Elimination Diets

As I’ve said, most patients we see do well using an elimination diet based on either a Paleo or low-FODMAP framework. However, some people may need stricter elimination diets like the autoimmune protocol (AIP) diet or a low-histamine diet.

The autoimmune protocol diet is a stricter version of a Paleo-style diet that also eliminates eggs and plants from the nightshade family, such as tomatoes and eggplant. The AIP is worth trying if you are still struggling with diverse symptoms after trying a Paleo diet and a low-FODMAP diet. 

Nightshades aren’t well studied, but there’s a possibility that they may worsen inflammation in some individuals with inflammatory bowel disease (IBD) or IBS [21].

Common nightshades you will need to eliminate on the AIP diet are bell peppers, chili peppers, eggplants, potatoes, and tomatoes. Some spices, such as paprika, cayenne pepper, chili powder, and crushed red pepper, are also made from nightshades and should be avoided. 

Alternatively, a low-histamine diet is an elimination diet that could benefit you if you have a lot of typical histamine intolerance symptoms, such as headaches, fatigue, mood swings, and skin rashes or hives. The main high-histamine foods to cut out on a low-histamine diet include aged cheese, fermented foods, and red wine.

If Your Gut Needs A Boost: An Elemental Diet

An elemental diet is the most restrictive type of elimination diet, but I still sometimes recommend it. An elemental diet is useful to cover your nutritional needs when you have severe gut symptoms that aren’t responding to a whole-food elimination diet. Following it for a few days gives your digestive system a rest so it can reset and potentially respond better to your elimination diet of choice. 

An elemental diet is a hypoallergenic liquid diet in which the nutrients are partially broken down, so your digestive system has less work to do. It comes as a powder that you simply mix, blend, or shake up with water. 

Getting Ready to Reintroduce Foods

Once you’ve been on an elimination diet for 3–4 weeks, you can follow this guide to determine where to go next. 

  • If your symptoms have improved significantly, you can move on to Step Two: the reintroduction phase. 
  • If your symptoms have improved somewhat, you may want to double down on your current eliminations for another couple of weeks. This means following your elimination diet a little more strictly while looking out for additional improvements. A month is the longest I would recommend you follow most types of elimination diet before you start reintroducing foods. Exceptions are the Paleo diet and low-FODMAP diet. A varied Paleo diet can supply adequate nutrition over the long term [22], and a varied low-FODMAP diet may be nutritionally sufficient for up to a year [23]. In any case, if you aren’t seeing additional positive improvements after a month but still feel a lot better than at the beginning, you should move on to Step Two.
  • If your symptoms did not improve much at all, you might want to move to the next type or level of elimination diet. For example, you might move from a Paleo diet to a low-FODMAP diet or from a low-FODMAP diet to AIP. You can even get more creative and combine two diets, say low-FODMAP plus low-histamine, if each one seems to help your symptoms somewhat. 

Take care not to stay on the more restrictive types of elimination diet (or combo of diets) for longer than a month. If you aren’t seeing positive improvements by then, you should move on to the next type of elimination diet, or consider that your symptoms may not be food-related. 

Step Two: Reintroducing Eliminated Foods

When you have found an elimination diet that calms your symptoms significantly, you may be tempted just to stay with that restricted diet because you don’t want your symptoms to return. You can do this with a varied Paleo diet, which can provide enough nutrition over the long haul [22]. And you can probably stay on a varied low-FODMAP diet for up to a year [23]. 

However, if your Paleo or low-FODMAP diet is very limited or you’re on a more restrictive type of elimination diet, this is not healthy for much longer than a month. Restrictive elimination diets may not have the full range of vitamins, minerals, and fiber your body needs in the long run. 

A restrictive diet can also affect you psychologically by, for example, limiting your social life and ability to eat out, or making you feel deprived.

It’s not a good idea to rush your reintroduction of potential trigger foods, but you don’t want it to be a long, drawn-out process, either. To help you figure out your pacing, these guidelines work for most people:

  • Reintroduce only one new food group at a time, allowing three days per food for sensitivity reactions or signs of intolerance to arise [24]. 
  • On the first day, have a small amount of the food group at one meal (some pasta, for example, if you’re testing wheat) and look for any symptoms in the next 24 hours. If you have no clear symptoms, it’s okay to be less cautious with how much of the reintroduced food you eat on the second and third day. This way, you can find out how much you can tolerate before having symptoms. 
  • If you do have significant symptoms, consider the food off-limits for now. After a strong food reaction, it also pays to have a couple days of washout (no more new foods) before moving on to the next 3-day food challenge. 
  • If applicable, experiment with different foods from the same group. For example, if you are introducing a specific FODMAP (say fructose, which is a monosaccharide, or M in FODMAP), you might want to try three different high-fructose fruits over three days—apples on day one, pears on day two, and mangoes on day three. Varying your reintroduction foods in this way may give you more insight into specific foods and help you widen your food palate more quickly. 
  • Keep a food diary or spreadsheet as you go, to facilitate tracking which foods cause symptoms like constipation, diarrhea, bloating, gas, and reflux. If you prefer to work with an app, Cara Care is a free one designed to help you see which foods are problematic and when. 
  • Don’t forget that with food sensitivities and intolerances, you may also have non-gastrointestinal symptoms such as rashes, hives, joint pain, brain fog, fatigue, anxiety, and headaches.

During the reintroduction phase, it’s important to go at your own pace and try not to stress too much (hard as this can be).

Also, be prepared to accept that some foods may never work for you, or that you may need to wait until you feel ready to try again, perhaps a few weeks or months down the road. 

If pinpointing exactly which foods you are sensitive or intolerant to is becoming too complicated, you might want to consider working with a trusted healthcare practitioner, like a dietitian, to help you through the process.

Be aware that your food reactions can ebb and flow before finally going away. The ups and downs reflect changes to your gut microbiome and immune system as your gut heals and becomes less inflamed by food triggers.

Generally, you don’t need to be too concerned about occasional mild symptoms along this journey.

Step Three: Maintenance (Moving Forward With a Balanced Diet)

Once you’ve identified the foods you can tolerate, you’ll have a new, personalized dietary framework for sustained symptom relief. The ultimate goal of a successful maintenance phase is to continue eating a diverse and nutrient-rich diet that helps you remain symptom-free over time.

However, as you move through the maintenance phase, it’s likely that the list of foods you need to avoid won’t stay set in stone. A few months into the maintenance phase, when your gut seems stable, you might want to retest the foods that remained problematic at the end of Step Two.

You may find that you can now tolerate more foods or larger amounts of prior irritants over time. Eating without (or with only minimal) symptoms may reflect that the burden on your immune system has declined and your gut has had more opportunity to heal. 

Support Maintenance With Probiotics

Probiotic supplements can be helpful for maintaining better gut health while your gut recovers from the impact of food intolerances. For example, probiotics can be effective at soothing irritable bowel syndrome symptoms, which are often the same as those of FODMAP intolerance [25, 26, 27, 28, 29].

Some studies also suggest that probiotics may help reduce the development and severity of classic immunoglobulin E (IgE) food allergies (like the allergies to peanuts or seafood I discussed above). They may do this by improving the health of your gut microbiota and calming your immune system [30, 31, 32, 33]. 

However, the evidence is still not clear-cut on how probiotics affect allergies [34], and we don’t yet know if probiotics are effective at helping with food sensitivities, such as non-celiac gluten sensitivity, that involve a milder immune response. 

Though the research is lagging behind, my clinical experience is that probiotics—particularly a combination of different types—do significantly help patients who are recovering from food sensitivities and intolerances.

The three probiotics that cover many bases and work together well are:

If you’ve tried one type of probiotic without noticing much benefit, I’d suggest that you give this triple therapy approach a try if you can. If it doesn’t help after a month, you can assume you probably don’t need probiotics right now.

3 Steps to Less Gut Discomfort

Elimination diets aren’t high-tech, and they aren’t perfect. But following the three steps of elimination, reintroduction, and maintenance is by far the best way to identify the food sensitivities or intolerances that could be causing your poor gut health. 

Maintaining a flexible approach and understanding that you might have a few obstacles along the way is a helpful mindset to adopt.

Most people can achieve success while working through an elimination diet by themselves, but you can also reach out to one of our experienced practitioners if you could use a helping hand. For a more rounded approach to better gut health, you can follow my 8-step plan in Healthy Gut, Healthy You.

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