A Functional Medicine approach to performing an elimination diet

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Embarking on an elimination diet can seem like a daunting endeavour. However, when guided by the principles of functional medicine, this process transforms into a powerful tool for uncovering the hidden causes of discomfort and disease.

In this article, we delve into the intricacies of an elimination diet, meticulously outlined to align with a functional medicine approach. We explore the common culprits of food sensitivities, why our bodies may react negatively to what we consume, and detail the process of eliminating and subsequently reintroducing foods.

By combining the elimination diet with functional medicine’s holistic perspective, we aim to empower you with the knowledge to not only improve your digestive health but also enhance your vitality and long-term health outcomes.


We are what we eat, but we are also what we absorb and a gastrointestinal system that is not functioning correctly can affect absorption of nutrients, but also how well we remove toxins and waste substances. Essentially our gut helps us absorb the good and remove the bad. The only trouble is when we are suffering with digestive dysfunctions like motility issues, intestinal permeability, inflammation, acid and enzyme deficiency, infections, overgrowths or general imbalances of bacteria, our ability to remove the bad and absorb the good becomes effected. When dysfunctions take place in the gastrointestinal system a whole host of symptoms can occur.

One thing that can severely effect how our gut functions and thus the function of the human body is the food we eat. Food reactions can occur on a number of different levels, and often these reactions are confused with one another. We can have allergies, usually IgE immune responses, these often cause more acute significant and fairly immediate reactions. We also have intolerances, these are often present because we are lacking something in our body to be able to process certain foods such as insufficient lactase to deal with certain levels of lactose, thus causing a lactose intolerance. We then also have food sensitivities. These can be much harder to determine because sensitivities whilst still can be immunological reactions are often much more mild, delayed and harder to determine.

There are various tests out there to try and determine different immune and inflammatory responses to foods. Some of which are good, many of which are vastly inaccurate and unreliable and some or which are quite expensive. At the time of writing this article there are no more than a handful of tests/labs that I would consider for food sensitivities.

One way around the use of food sensitivity testing and generally regarded as the gold standard is the use of a method called the elimination diet. No one really likes to change their dietary habits, however when digestive, immune or other inflammatory or unexplained symptoms are persisting and food reactions are suspected this is one of the most successful and accepted methods.

The main downfall of this approach is the strict adherence required for the programme to be successful. It is no easy task to stay 100% adherent to the programme, however the benefits can be quite profound. I have found elimination diets extremely useful in cases such as chronic headaches and migraines, poor skin health, IBS, IBD like crohn’s and colitis, inability to drop fat even in a calorie deficit, water retention issues, autoimmune conditions, eczema, rheumatoid arthritis and so on.

In this article I am going to take you through the process of an elimination diet and how to achieve success when performing it.


Where to start with an Elimination Diet

Here are the tools I would give my clients when performing an elimination diet.

  1. Food and Symptom Diary – You will record and track your food and symptoms throughout the process.
  2. Food Lists – lists that provide foods that are okay to eat and ones that should be avoided.
  3. Information on how to properly challenge test the body.

I tend to use a modified version of an elimination diet where we first of all avoid the foods or family of foods we are most suspect of causing any dysfunctions. To do this you must first assess whether any of your symptoms are bought on around certain types of foods. I will also look at a completed food diary with my clients to understand what foods they eat most frequently. Often times it is the foods that we eat all the time that cause reactions in the body.


What are the most common foods to cause problems?

The most common foods that cause reactions tend to be:

  • Grains, especially gluten containing grains, this can include, wheat, barley, rye to name a few.
  • Dairy, especially cow’s milk based dairy. On occasions people can tolerate goats and sheep’s, even though they react poorly to cow based foods.
  • Eggs, probably because eggs can often be consumed on a daily basis, especially by those on vegetarian based diets or those trying to increase protein in their diet.
  • Soy, again often a hidden ingredient in many foods or over consumed by certain populations.
  • Nuts, I have seen numerous reactions to nuts, mostly due to an over consumption.

Generally speaking fruits and vegetables are very hypoallergenic, meaning they are unlikely to cause an issue, although I have seen reactions to almost any food available so you have to keep an open mind. Generally the goal is to remove the big players, the foods that are causing the most significant reactions.


What foods should you remove in an elimination diet?

When someone comes to me with digestive issues, two food groups I am most likely to suspect are gluten containing foods and dairy, especially cow’s dairy. I then look at their food diary and assess what foods they are eating on a regular basis. Those that are regularly added to the food diary (daily or even multiple times a day), are foods I am more suspect of.

Here is my top 5 list of foods to remove

  • Gluten
  • Cow’s Dairy
  • Alcohol
  • Caffeine
  • Processed Sugar

After that I also consider the removal of the following depending on how frequently they feature in someones diet

  • Soy
  • Nuts (I might be specific with what nuts)
  • Eggs (Typically chicken eggs only)

One of the important steps of an elimination diet is to focus on the foods that you can consume. This way you focus on the positive rather than being wrapped up in the negative.

You will be surprised at home many foods you can still consume even after removing all the above. But yes, it is going to take some time to plan what you are going to eat. Equally, you are not going to just be able to grab things on the go very easily or eat according to past default habits. For this reason, doing an elimination diet is challenging.


Can you experience any negative reactions on an elimination diet?

There can sometimes be negative reactions experienced when performing an elimination diet, but more often than not these are reactions from coming off of certain offending or addictive foods. Sugar, caffeine and alcohol withdrawals are common, and will often cause headaches and irritability.

It is also important that you don’t just eliminate foods and drop your calorie consumption levels too low. It is not uncommon to lower body fat on this diet especially if you have been used to eating large amounts of processed foods and grains, however what we do not want to do is stress the body by feeding it insufficient calories over a sustained period of time. An elimination diet is not a weight loss strategy, although in many instances it will help.

It is always a good idea to give it around 7-10 days to allow for any of the new symptoms to subside and then reassess. If symptoms persist beyond that then changes to your food choices should occur and support may be required.


How long is the elimination diet?

Presuming that the modified version of the elimination diet has subsided the symptoms you were experiencing, then after around 4 weeks you may want to start to challenge the body with some of the foods you eliminated. I tend to leave the most obvious foods till last before introducing back in, these tend to be gluten, dairy and eggs.

If you have eliminated a number of foods and still have not seen an improvement in symptoms then in my eyes this is the time to test. If something is going wrong with digestion then there are generally one of, or a combination of the below possibilities.

  • There is something in your gut that should not be – Bad bugs (parasite, yeast/fungal overgrowth, pathogenic bacteria etc).
  • You are still putting something in your mouth that you should not be. Possibly one of your allowed foods is still causing problems for you or you did not follow the program to the letter.
  • There is not enough of something in your gut that should be. This is generally enzymes, acids, good bacteria.
  • Your external environment and nervous system are impacting the function of your gut. Effectively, looking at how stress is impacting on the function of your gut.


What is the reintroduction process on an elimination diet?

After you have been through the first 4 weeks you can then start to reintroduce foods back in. This should be done in a controlled manner that looks for cause and effect. Here are the key points to the reintroduction process.

  1. Choose the next food on the current band list that is the most hypoallergenic food.
  2. Make sure you use your food and symptom diary to assess any negative reactions.
  3. Eat the newly introduced food 2 times in one day, then remove the food again for the next 4 days and continue to eat as you did previously on your elimination diet in the first 4 weeks.
  4. Over the subsequent 3-4 days after the challenge day look for any negative reactions, and subsequent negative reactions should make you suspicious of that food. Symptoms include things like changes in: Energy Levels, Digestion, Sleep, Skin, Mood, Joint pain, headaches and cognitive function etc.
  5. Only introduce one food at a time, and wait for any symptoms to subside before challenging with another food.
  6. Any food that a negative reaction occurs should be kept on the excluded list for the time being.
  7. Any possible reactions should be retested to make a final judgement.

I’ve finalised my foods to include and foods to avoid list, now what?

Some thought should be given to what might have caused these reactions in the first place. Often our digestive system can become stressed when we are under stress, causing significant reductions in certain enzymes and acids, and in some cases causing increased risk of intestinal permeability, also known as leaky gut, making you more susceptible to food reactions. As always it is about individualising your approach as much as possible and trying to determine what the triggers might have been.

Common triggers to food sensitivities include:

  • Alcohol
  • NSAIDs (anti-inflammatory drugs)
  • High Stress (emotional and physical)
  • Nutritional Deficiencies such as zinc, healthy fats, vitamin A
  • Excessive consumption of pro-inflammatory fats
  • Intestinal bacterial imbalance or pathogenic bugs

Addressing the potential underlying cause is the most important part of this process. By doing that you are often able to reintroduce many foods that you may never have a problem with again in the future.

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