Site icon The Nutrition Clinic for Digestive Health

Help, I Don’t Know What to Eat – The Elimination Diet Guide

Woman doing grocery shopping at the supermarket, she is pushing a cart and checking a list

Woman doing grocery shopping at the supermarket, she is pushing a cart and checking a list

Table of Contents

What is an Elimination Diet

An elimination diet is an organized way to remove potentially problematic foods from someone’s diet. If you’re suffering from digestive problems, an elimination diet should be one of the first things you try.

Because food sensitivities and food allergies are more common now than ever, elimination diets can be effective for many people (1).  

Elimination diets are non-invasive, low cost, and pose a very low risk of harm. 

There are several different elimination diets to choose from. This blog post aims to provide information and resources on the best elimination diets. We also discuss who is and is not a good fit for each elimination diet.

When is an Elimination Diet Helpful?

Adverse food reactions can cause symptoms just about anywhere in the body! If you have symptoms that don’t seem to resolve with conventional approaches and can’t otherwise be explained, it might be worth trying an elimination diet to see if you can get some relief.

Common symptoms of adverse food reactions include:

  • Fatigue 
  • Insomnia 
  • Anxiety 
  • Mood swings 
  • Food cravings 
  • Brain fog 
  • Headaches 
  • Migraines 
  • Tinnitus (ringing in the ears) 
  • Sensitivity to sound
  • Rashes or hives 
  • Eczema or psoriasis 
  • Flushing 
  • Itchy skin 
  • Sinus issues 
  • Canker sores 
  • Lung congestion 
  • Red, swollen, watery, or itchy eyes 
  • Sensitivity to light
  • Urinary tract issues 
  • Joint pain or stiffness 
  • Muscle pain, spasms, or cramps
  • Irregular heartbeat 
  • High blood pressure 
  • Heartburn or reflux 
  • Stomach or intestinal pains or cramps 
  • Constipation 
  • Diarrhea 
  • Bloating 
  • Gas or burping 
  • Nausea 
  • Vomiting 
  • Painful elimination 
  • Fluctuating weight
  • Water retention 

How to Do an Elimination Diet

The Elimination Phase

During the elimination phase of an elimination diet, foods suspected to be problematic are removed for some time and then reintroduced when symptoms have improved. 

And by removed, we mean REMOVED! Even very small amounts of problematic food can cause symptoms. So we’re sorry, but that low dairy diet you tried wasn’t dairy-free. 😉

For someone with food sensitivities or food intolerances (which you’re about to learn are two different things), removing problematic foods can help manage symptoms. 

Why you may feel worse when starting an elimination diet
  1. When problematic foods are removed, the body finally gets a break from the damage caused by inflammation. It can now get to work to heal and repair. Healing and recovering require energy, which can leave you feeling quite tired.
  1. Certain foods, like gluten, dairy, and soy, can have an opioid-like effect causing us to feel good when we consume them. If they’re also problematic, the opioid effect can mask their negative impact on our bodies. When these foods are removed, and that opioid effect is gone, we’re left to heal and recover without the pain-reducing effect (2). 
  1. Some foods (like those with a high glycemic index) increase the production of serotonin and endorphins; when we stop consuming them, the production of these “feel-good” hormones decreases (3).
How long does it take to get results on an elimination diet?

If you don’t get any improvement within two weeks, it’s safe to say your diet isn’t working. Elimination diets aren’t meant to be permanent. They should be used as a tool to get symptoms under control and establish a healthy baseline. 

The Reintroduction Phase

With every elimination diet, the elimination phase should be followed by a reintroduction phase. 

Once the problematic foods have been removed (assuming you removed all of the right things and did so correctly), you should feel significantly better.

The goal should be to systematically liberalize your diet as much as possible, only avoiding what is necessary.

You’ll likely be able to tolerate some of what was removed and easily identify the truly problematic foods when you add them back in.

Adding foods back is an experiment to help you figure out what made you feel bad (so you will be looking to provoke symptoms upon reintroducing foods).

During the reintroduction phase, keeping a food journal and tracking your symptoms are important.  This helps to identify patterns so you can figure out which foods are problematic for you!

If you cannot reintroduce any of the eliminated foods, other interventions and further testing might be necessary to find and address the root cause of your symptoms.

Food and Symptom Tracking Resources:

Elimination Diet Side Effects

Elimination diets should be used short-term to determine if food is causing adverse reactions. Following an elimination diet for long periods can have unwanted consequences.

Help! My elimination diet isn’t working!

An elimination diet can be an effective way to address various health issues. Sometimes it’s enough, and sometimes more digging needs to be done. 

If your elimination diet isn’t working, here are a few things to troubleshoot: 

If you’ve considered all of the above troubleshooting tips and still don’t feel better, check out the graphic below.

Everyone’s path to feeling better looks different – some people do well with an elimination diet followed by a good probiotic. Others are more complicated and require a full workup of functional testing and heavier supplementation until they can get to the root cause of their digestive issues.

A step-by-step approach to healing your gut

If an elimination diet isn’t enough to get you feeling better, digestive support can be added. This could include supplements such as enzymes, apple cider vinegar, gall bladder support, probiotics, and prebiotics.

If you can’t figure out the right amount of digestive support or supplements make you feel worse, it’s probably time to add in some functional nutrition testing. You can follow a targeted intervention based on your test results.

The Differences Between Food Allergies, Food Intolerances, and Food Sensitivities

Although these terms are used interchangeably, there are big differences between food allergies, food intolerances, and food sensitivities. 

Here’s a reference chart highlighting the main differences; additional information can be found below.

Immune System Involvement Common foodsOnset of symptomsCommon Symptoms Treatment Testing 
Food AllergyIgE antibodies,
mast cells,
pro-inflammatory mediators 
Tree nut, Shellfish, Fish, Sesame 
Within minutes to hours hives,
trouble breathing, swelling
Avoid food completely – typically lifelong  Skin Prick Test 
Food Sensitivity IgG,
pro-inflammatory mediators,
White blood cells 
Any food or chemical – can be dose dependant  Up to 72 hours after consumptionCan affect the entire body: Diarrhea, constipation, stomach pain, muscle and joint pain, seasonal allergy-like symptoms (runny nose and sneezing), fatigue, mental and emotional distress, brain fog, rashes, hives, headaches Avoid for a period (typically 1-6 months) of time and then reintroduce – can change.  MRT 
Food IntoleranceNot immune-mediated – related to not being able to break the food down properlyLactose, histamine, FODMAP, sulfur Varies from minutes to days Bloating,
diarrhea, constipation,
stomach pain,
greasy stool,
excessive or odorous gas
Avoid for some time (typically 1-6 months) and then reintroduce – can change. Testing for individual intolerance is available (ex: lactose tolerance test)
This chart shows the key similarities and differences in food allergy, food sensitivity, and food intolerance.
The lining of a gut in someone without food allergies, versus the lining of a gut in someone with food allergies. The gut lining in someone with diagnosed food allergies is weaker and more permeable.

Food Allergies

A food allergy is the body’s reaction to typically harmless foods that causes the immune system to produce IgE antibodies in response to proteins found in specific foods.

9 Most Common Food Allergies 

Tree nut









Food Sensitivities and Food Intolerances

Food Sensitivity

A food sensitivity occurs when the body begins an immune-mediated response to certain foods. Food sensitivities do not result in IgE antibodies (making them different from food allergies).

Food sensitivities involve the activation of the immune system, so a wide range of symptoms can develop.  

Food Intolerance

A food intolerance occurs when your body has difficulty breaking foods down, resulting in digestive symptoms ONLY.

Food sensitivities and intolerances can develop for several reasons (see below) but aren’t necessarily lifelong, and they don’t have the potential to become immediately life-threatening like a food allergy. 

Conditions associated with food sensitivities

Food sensitivities and intolerances occur due to: 

Why Are Food Allergies on the Rise?

There are several theories for the increase in allergies and sensitivities: 

Hygiene Hypothesis

Dual Allergen Exposure Theory

The dual allergen exposure theory postulates that common allergen foods should be introduced early (between 5-11 months) during weaning to establish a tolerance (7).  

Vitamin D Deficiencies 

Vitamin D deficiencies, partially due to more time spent inside, have also been linked to an increased likelihood of food allergies (8).  This is because vitamin D helps to regulate the immune system.

Interestingly, vitamin D levels shouldn’t get too high as this can also increase the development of food allergies (9). 

We recommend monitoring your vitamin D levels with a goal of 50-80 ng/ml.

Increase in Chemical Exposure

In the common Standard American Diet (SAD as it is accurately called), we are exposed to many more chemicals now through the intake of processed foods than ever before. 🤮

The theory is that this increased chemical load alters the immune system by making the detoxification organs work overtime. 

Food Sensitivity Testing 

Since elimination diets can address food sensitivities, we’re reviewing food sensitivity testing here. 

IgG Testing 

Companies like EverlyWell and Pinnertest use IgG testing. IgG is the most widely available option because it’s very cheap and quick.

P88 Dietary Antigen Test

This test offered by Precision Point Diagnostics includes IgE, IgG4, and complement (C3d) testing along with IgG to measure allergies and sensitivities.  Complement activation is thought to amplify the immune system’s response, resulting in more severe inflammation and symptoms (13). 

While this test is a much better option than one solely measuring IgG, it’s not our favorite.  

MRT Food Sensitivity Test

MRT stands for Mediator Release Test. This is what we use in practice – when the test results are combined with the right dietary protocol, our clients get really good results.

Here’s why we love MRT for food sensitivities:

Scientific studies supporting the MRT test include: 

The research process is long and tedious. We’re so excited to have more studies on MRT in progress. Currently, the following conditions are being studied using MRT as an intervention:

In our clinical experience (along with hundreds of other clinicians using MRT), using the results from this test dramatically reduces inflammation, decreasing symptoms for the majority of our clients.   

According to the Academy of Nutrition and Dietetics, “when peer-reviewed scientific studies are lacking, we must rely on expert opinion and experience.” 

Elimination Diet Plans 

The timeline for an elimination diet varies based on the type of diet you choose, the severity of your symptoms, and your goals

You might feel worse at the beginning of an elimination diet before you start to feel better. As we said before, if you’re not doing significantly better after 14 days, it’s time to reassess

Now, let’s dive into the details on elimination diets we use and who they are appropriate for (and who they aren’t). 

LEAP Food Sensitivity Testing Protocol

The LEAP Protocol is a personalized anti-inflammatory diet.

Our dietitians work with clients to create a personalized elimination diet based on their test results.

We recommend preparing all of your food at home for the first several weeks. This reduces the chances of cross-contamination and accidentally eating foods that aren’t on your plan. 

Who needs a LEAP diet?

This is a good fit for you if you’re…

Is the LEAP diet good for everyone?

This isn’t a good fit for you if you’re…

LEAP MRT Resources


FODMAP is an acronym for Fermentable Oligosaccharides, Disaccharides, Monosaccharides, And Polyols, which are different groups of carbohydrates consumed in most diets.

Each FODMAP group is further broken down, and specific foods fall into the sub-categories. Oy!

Here are a few examples to make this more relatable (this is not a full listing for each group).

Oligosaccharides (Fructans + galacto-oligosaccharides (GOS))
Wheat, barley, rye, onion, garlic, beans
Monosaccharides (Fructose)
Pears, honey, apples
Disaccharides (Lactose)
Milk, ice cream, cottage cheese
Polyols (Mannitol + sorbitol)
Sugar-free gum, avocado, corn, mushrooms, cauliflower
FODMAP groups and corresponding foods – non-comprehensive list

Removing high FODMAP foods from the diet has been shown to greatly relieve GI symptoms for individuals with: 

FODMAP groups and corresponding foods.

How to Do Low FODMAP diet  

Following a low FODMAP diet means you are keeping your total FODMAP load to a minimum by limiting high FODMAP foods.

To explain this process, picture a bucket. 

Each time you eat, you add FODMAPs to your bucket. When your bucket overflows, digestive symptoms occur.  

It’s very much a dose/response relationship.

To stay organized and clear on how FODMAPs affect you, this diet is divided into phases.

FODMAP Elimination Phase

During this phase, you eliminate high FODMAP foods.

FODMAP Reintroductions – the challenge phase

When you add FODMAPs back to your diet in the challenge phase, you’re trying to determine how many FODMAPs you can fit into your bucket before it overflows. 

The ultimate goal is to get you feeling your best with the least amount of dietary restrictions. 

Having an intolerance to one or two groups of FODMAPs isn’t reason for concern (especially if one of them is lactose). 

If you can’t tolerate any high FODMAP foods after the elimination phase, you’ll need to do more digging to address the root cause of your FODMAP intolerance.

Because this can be a difficult diet to follow correctly (and reintroduce correctly), we recommend working with one of our registered dietitians to get the best results. 

Underlying causes of FODMAP intolerance include:

Who needs a Low FODMAP diet?

This is a good fit if you…

Is a Low FODMAP diet good for everyone?

This isn’t a good fit if you…

Low FODMAP Resources

Of all the diets we counsel clients on, this is the one people think they are following correctly but usually aren’t.

Getting portion sizes right on this diet is critical to success, as is following trusted resources. Several FODMAP resources are out there, and many conflict with each other.

Before you give up following a low FODMAP diet, consider working with a professional (such as one of our dietitians) with FODMAP diet experience.

AIP Elimination Diet

The autoimmune protocol diet (or AIP), developed by Dr. Sarah Ballantyne, is a more restrictive version of the commonly used Paleo diet.  Going beyond the Paleo diet of eliminating grains, dairy, and legumes, the AIP diet also removes foods suspected to contribute to autoimmune issues. 

AIP Elimination Phase

GrainsArtificial sweetenersNuts and seedsCoffee
EggsNightshade vegetables*DairyAlcohol
LegumesOverly processed oilsFood additivesNSAIDS
Foods removed during the AIP diet elimination phase

* Nightshade vegetables include tomatoes and tomato-based foods and products, tomatillos, potatoes, eggplant, peppers (bell peppers, jalapeno, chili peppers, and hot peppers), red spices (curry powder, chili powder, cayenne powder, red pepper, paprika), pimentos, tobacco, goji berries, ground cherries, and ashwagandha).

If you’ve been on the AIP diet for three months and still have symptoms, it is time to meet with one of our registered dietitians to help identify missing links! 

Who needs the AIP diet?

This is a good fit if you…

Is the AIP diet good for everyone?

This isn’t a good fit if you…

AIP Elimination Diet Resources

There are so many amazing resources out there for the AIP diet; here are a few of our favorites:

Whole 30

The Whole 30, created by Melissa Urban, is a very common elimination diet that cuts out foods associated with food sensitivities (i.e., gluten and dairy) and food intolerances (i.e., beans and legumes and soy).

Phases of Whole 30

Foods RemovedReason for removal
Grains (3233Can increase gut permeability and be hard to digest 
Legumes (34These are high FODMAP which makes them difficult to digest
Dairy (3560-70% of the world has lactose intolerance 
Added Sugar (36Increases cravings, alters blood sugar,
competes with the consumption of nutrient-dense food,
associated with inflammatory conditions
Alcohol (37Large amounts can damage the GI tract
Added chemicals (carrageenan or sulfites)Found in processed foods, which promote inflammation and lack nutrients

Who needs the Whole 30 diet?

This is a good fit if you…

Is the Whole 30 diet good for everyone?

This isn’t a good fit if you…

Whole 30 Recipes and Resources

Healing Gut Diet 

We designed the Healing Gut Diet with our clients in mind 😃.

This diet removes foods that make it difficult for the gut to heal and adds in foods that are easy to digest and anti-inflammatory. 

Anti-inflammatory foods on this meal plan include: 

For a more detailed description of why we recommend removing the foods in the chart below, start with our blog post on the Healing Gut Diet

GlutenQuinoa, oats, rice, corn 
Dairy Nut milk alternatives
Added SugarCacao nibs, freeze dried fruit 
Raw Veggies Cooked vegetables, soups, slow cooker meals, smoothies
AlcoholCollagen Peptides, Bone broth, Gelatin 
Healing gut diet healthy swaps

Because it can take anywhere from three months to a year for someone’s gut to heal and because you’re not at risk for nutrient deficiencies, you can stay on this diet longer than others described in this post.  

We recommend starting with one month, and if you do not feel significantly better, then it is time to get support from one of our registered dietitians.

Who needs the Healing Gut Diet?

This is a good fit if you…

Is the Healing Gut Diet good for everyone?

This isn’t a good fit if you…


Gluten-free and Dairy-free

Lastly, we wanted to touch on the most basic elimination diet, going gluten-free and dairy-free. 

Common sources of gluten

Gluten-containing grains

Be sure to read food labels and avoid these ingredients when eliminating gluten:

  • Barley
  • Barley malt/extract
  • Bran
  • Bulgar
  • Couscous
  • Durum
  • Einkorn
  • Emmer
  • Farina
  • Farro   
  • Graham flour
  • Kamut
  • Matzo flour/meal
  • Orzo
  • Panko
  • Rye
  • Seitan
  • Semolina
  • Spelt
  • Triticale
  • Udon
  • Wheat
  • Wheat bran
  • Wheat germ
Hidden sources of gluten

Some of the above may seem like obvious sources of gluten. But, gluten can also be sneaky – lots of times, it’s hiding in foods and even non-food products that you may not suspect.

Food products that can contain gluten:

These may or may not contain gluten, label reading is essential to ensure you’re gluten-free. Companies can change ingredients in their products, so be sure to check labels often.

Beer and lagersBread crumbsSelf-basting poultry
Soup bases (like bouillon cubes)Pasta Brown rice syrup
Drink mixesBrothCured pork products 
Lunch meatSoy sauceCommunion wafers
MarinadesCroutonsImitation meat
Seafood coating mix     GravySauces
ThickenersCakes, cookies, doughnutsIce cream cones  
Food products likely to contain gluten

Non-food products that can contain gluten:

These may or may not contain gluten, it’s advised to check the ingredient labels to ensure you’re gluten-free.

Supplements Playdough
Medications (prescription & OTC)Lipstick, lip gloss, chapstick, lip balm
LotionStamps and envelope glue
Mouthwash & Toothpaste
Non-food products that may contain gluten

Common sources of dairy

Dairy doesn’t require quite the diligence gluten does to remove from your diet. However, the list below is still worth reviewing. Be sure to avoid these when eliminating dairy:

Half & halfWheyCasein
Sweets *
(chocolate, baked goods, packaged foods)
Cottage cheeseProtein bars*
Granola bars*Whey protein powder
Foods and ingredients to avoid on a dairy-free diet
*may contain dairy

Who needs a Gluten-free and Dairy-free Diet?

This is a good fit if you…

Is a Gluten-free and Dairy-free diet good for everyone?


We always recommend starting with diet and lifestyle changes when trying to heal your gut. 

Sometimes, an elimination diet is all you need to feel better.  But, sometimes, an elimination diet isn’t enough. That’s when it becomes time to look for underlying imbalances that need to be addressed.

Underlying imbalances that cause adverse food reactions can include: 

When the body is balanced, and the gut is healthy and functioning the way that it should, food shouldn’t cause problems.

Are you ready to finally heal your gut?

Schedule your FREE 15-minute phone call today!

Just click below to schedule online!

Prefer the phone? Just call or text 678-424-6520

Exit mobile version