Elimination Diets – Pinpointing the Source of Undiagnosed Symptoms

Hippocrates once said that “all disease begins in the gut”, and as it is now widely considered that 70% of the immune system is located in the gut, his statement may not have been too far from the truth. Indeed, research is now frequently suggesting that poor gut health is closely associated with the development of many of today’s most prevalent chronic diseases.

Food sensitivities and allergies  are two of the most  frequent yet enigmatic contributory factors associated with poor gut health – they carry unpleasant symptoms and often go undetected. There are a number of methods to detect food sensitivities and one of these is an elimination diet; which is considered to be the ‘gold standard’ for identifying problematic foods. In this week’s article we are looking at how to efficiently and effectively partake in an elimination/re challenge diet.

Difference between Food Allergy, Food Sensitivity and Food Intolerance

“One man’s food is another man’s poison” is a saying that is centuries old but one which speaks volumes in terms of emphasising the individuality of us all and how we each react differently to certain foods and drink. The purpose of an elimination diet is to expose and pinpoint the source of any undiagnosed symptoms that you are experiencing, as these symptoms can often be down to a ‘food allergy’, ‘food sensitivity’ or ‘food intolerance’; each of which is a term used interchangeably, but they are in fact all different.

Food allergy: This is a rapid response by the body’s immune system to a particular food and is mediated by IgE antibodies. These are  antibodies that trigger immediate allergic reactions binding to basophils (a type of white blood cell) in the bloodstream and mast cells in tissues. When basophils or mast cells with IgE bound to them they release substances such as histamine resulting in inflammation.

Severe food allergies can be life threatening and include anaphylactic shock. Please note that if food allergies are suspected then an elimination and re-challenge diet is not recommended, except under medical supervision.

Food sensitivities: In the case of  food sensitivities, symptoms can be slow to develop, often taking hours or even days to appear. Food sensitivities and reactions have been linked to conditions such as:

  • autoimmune disorders
  • skin conditions
  • asthma and allergies
  • migraines
  • atherosclerosis and other cardiovascular diseases
  • mood disorders
  • arthritis
  • addiction
  • kidney problems
  • narcolepsy
  • neurodegenerative diseases such as dementia
  • and many more

Food intolerances: These can be due to an autoimmune process e.g. coeliac disease or a lack of the necessary enzymes to process the food eg lactose intolerance (due to a lack of the enzyme lactase).

What is an elimination diet?

An ‘elimination diet’  is a short term eating plan that aims to remove suspect foods from your diet, for between 3 weeks and 3 months, and then slowly introduce them back into your diet one at a time, whilst monitoring and recording your symptoms before and during the elimination and after re-challenge.

How does it work?

 There are various levels of elimination – which we are referring to as ‘Basic’, ‘Comprehensive’, ‘Autoimmune’ and ‘FODMAPs’.

  1. Basic Elimination would consist of eliminating gluten, and perhaps dairy, which are commonly found to be problematic for many people. This can be a good starting point for people as, with planning, it is possible to find alternatives to these foods. It is important to ensure removal of all sources and gluten is often found hidden in many foods including rice sushi, soups, restaurant chips and some types of soy sauce.
  2. Comprehensive Elimination would include removing gluten, dairy, soy and eggs, citrus and possibly other grains (such as oats, rice) and pseudograins (such as buckwheat and quinoa).
  3. Autoimmune Elimination would involve removing gluten, all other grains, dairy, soy, eggs, other beans/pulses, nuts and seeds and deadly nightshade (potatoes, tomatoes, aubergines, peppers, chillies).
  4. FODMAPs – fructo-, oligo-, di-, monosaccharides and polyols. These are types of carbohydrates found in some fruit, vegetables, cereal grains and dairy. They can ferment in the gut and be a cause of bloating and IBS. We have previously written on FODMAPs and won’t specifically be talking about them in this blog, but the elimination methodology below would be similar.

This is not a comprehensive list of types of elimination diet – any food that is suspected of causing a problem could be eliminated for a short while and then reintroduced.

 Foods to Include and Exclude during an Elimination diet

Whichever exclusion you choose to do – also exclude sugary foods and processed vegetable oils including margarines.

Type of Elimination Diet Foods to Include Foods to Exclude

Basic – Dairy and Gluten


All vegetables and fruit, nuts/seeds, meat, fish, eggs, olive oil, coconut milk, coconut yoghurt, oats, rice, buckwheat, (gluten free breads etc in moderation*)


Dairy – milk, yoghurt, butter, cheese, whey. Check food labels.


Gluten – wheat, barley, rye – bread, pasta, cous cous, some soy sauce, Worcester sauce, some rice sushi, pub chips, flour products. Check ingredients. Ask in restaurants.



Comprehensive Elimination


All vegetables and most fruits, nuts/seeds, meat, fish, olive oil, coconut milk, coconut yoghurt, sweet potatoes


Gluten, dairy, soy (soy milk, cheese, yoghurt etc), eggs, citrus and possibly other grains (oats, rice, corn) and pseudograins (buckwheat, quinoa)


Autoimmune Elimination


Most vegetables (except deadly nightshade), Sweet potatoes, Most fruit, Meat, Fish, Olive oil, Coconut products (check some coconut milks contain rice), Herbal tea, Green or black tea, Coconut milk kefir, Herbs and spices (not chilli)



Dairy, Gluten, Eggs, Soy ,All Grains, All Pseudograins, Deadly nightshade vegetables (potatoes, tomatoes, aubergines, peppers, chillies), Nuts/seeds,, Beans/pulses, Alcohol, Coffee


*If conducting a gluten-free elimination, avoid over-consuming commercial ‘gluten free’ foods. These foods can be useful for convenience but are often highly processed and lacking in essential nutrients. If eliminating all grains then gluten-free breads etc would also need to be eliminated.

Although this may seem like a lot of foods to remove from your diet, the more you actually remove, the more likely you are to find out which food is causing the health-related issue in your body.

Most elimination diets last for around 3-6 weeks as the antibodies (proteins your immune system makes when it negatively reacts to foods) take around three weeks to clear, although sometimes it is recommended that foods are removed for up to 3 months to see the full benefit.

Once these have been removed, you should begin to see an improvement in your symptoms.

Elimination methodology

  • In the week before you begin the elimination diet monitor and record your symptoms while eating your usual daily diet.
  • During the period of elimination eat ONLY the foods on the ‘allowed’ lists – (see table above for foods included and excluded depending on the type of elimination you are doing). It is important that the elimination is 100% to get the best results – so check all food labels.
  • When eliminating foods focus on the foods you can eat, rather than those you cannot.
  • Plan your diet for the elimination period – all meals and snacks.
  • Carry a sheet of foods you can eat with you, as a reminder.
  • Monitor and record your symptoms during the elimination phase and compare them to before you started.

Challenge / Reintroduction Phase

After your chosen time period of eliminating these foods, you need to reintroduce foods, one at a time and watch for reactions. If you have removed a lot of foods this may take some time. Leave gluten, grains and dairy until last. Other than that reintroduce foods from each food group eg nuts, seeds, beans, lentils, tomatoes, peppers, one group at a time.

It is important to note that this is a process that should not be rushed – in order for your elimination diet to be successful, patience and close monitoring of symptoms and bodily reactions, is essential.

  • After your chosen period of elimination, which should be at least 3 weeks, reintroduce foods one at a time and continue to monitor and record symptoms.
  • Continue to eat all the foods on the allowed list.
  • Do only one challenge at a time ie foods from one group eg nuts.
  • On the day of the challenge, eat a small portion of the food.
  • If you feel unwell during the challenge, return to the elimination diet and try the challenge again when you are feeling well again (it could be coincidence that you felt unwell, so recheck the result).
  • Always allow at least 3 days on the elimination diet between each new food challenge, longer if you suffered constipation or if the challenge phase provoked symptoms.
  • When you are ready, and feeling well, select and carry out the next challenge.
  • Leave grains, gluten and dairy until last as these are foods that most often cause a reaction. Other than that, the order of the challenges doesn’t matter. Do the one that is the most important to you first and leave the foods you can easily do without for last.
  • Record everything – what you ate during the challenges (including portion sizes) and any symptoms.
  • If you don’t react to a food challenge within 3 days then that reduces the likelihood you have a problem with that food group – however keep it out of your diet until all the challenges have been completed. This is because with some foods there may be a cumulative effect and symptoms only become apparent after several days of eating it – so this could affect the results of other challenges.

Evaluate your results

  • If particular foods are a problem for you, you should now have an idea which foods trigger certain symptoms. Continue to avoid these foods.

Healing the Gut

Once you have conducted an elimination and challenge diet it is important to carry out some gut healing if you have reacted to certain foods. See our Leaky Gut blog on how to go about this.

What about nutrient deficiencies during an elimination?

The risk of missing out on important nutrients partly depends on what foods are being eliminated and how long the elimination is being carried out. During the elimination ensure you are eating as many different types of food as possible from the allowed foods list.

An autoimmune elimination diet without grains and nuts could be low in certain B vitamins (especially B6). A good all round multivitamin/mineral would be important to include during an elimination diet, possibly with extra B vitamins.

Calcium might be another concern if dairy and nuts are eliminated. Other good sources of calcium are dark green leafy vegetables, sardines with the bones mashed in and fortified coconut milk (available in cartons in the long-life section).

Benefits of an elimination diet

Identifying and removing food sensitivities / allergies can improve many conditions as these examples show:

IBS – A study at the University of Kansas medical centre monitored 20 patients with irritable bowel syndrome (IBS) all of whom underwent elimination diets as part of a 2006 study – 100 percent of these patients experienced significant improvements in digestive symptoms.

“These data demonstrate that identifying and appropriately addressing food sensitivity in IBS patients not previously responding to standard therapy results in a sustained clinical response and impacts on overall well being and quality of life in this challenging entity.”

Eosinophilic Oesophagitis – Further research involving 52 patients cut out four major food-allergen groups for a six-month period: dairy products, wheat, eggs and legumes – the results indicated that “A six-food group elimination diet (SFGED) achieves remission in more than 70% of adult patients with EoE.”

“Milk was identified as an EoE trigger in 11 patients (50%), egg in 8 (36%), wheat in 7 (31%), and legumes in 4 (18%). All patients had just 1 or 2 food triggers, with milk being the only causative food in 27% of the patients.”

The patients had no idea that they were allergic to any of the above foods – so many trips to the local GP were wasted as there was no way of getting to the cause of the problem. A simple elimination diet pinpointed the problem directly, and through elimination of these foods the patients in the study are no longer experiencing symptoms.

Skin irritations such as eczema and acne have also been linked to undiagnosed food allergies as research suggests:

“We have evaluated the relationship between eczema and food by using elimination diet and subsequently open and double blind challenge test in 15 patients. The clinical manifestations of 14 subjects were improved by elimination diet. Challenge test was positive in 10 patients. Nuts, tomatoes, milk, eggs and cereals were most frequently involved. Six patients suffered from food allergy (F.A.), 4 patients from food intolerance (F.I.) and 4 patients from suspected F.I. With the use of dietary elimination procedure the symptoms completely disappeared. The results obtained for the treatment of eczema with this procedure may be very encouraging.”


As you can see identifying food sensitivities and allergies is a little like forensics! When properly planned though, it can pay dividends in terms of improving symptoms and pinpointing an exact issue – in which case the time and effort will all feel worthwhile.

As explained, the aim is to reintroduce non problematic foods – not remain on a very restricted diet for ever.

It is also important to carry out some ‘gut healing’ work, otherwise further food sensitivities may develop. There are many nutrients important for gut healing including – vitamin D, vitamin A, essential fatty acids, live bacteria, curcumin and L-glutamine -and this is discussed further in our previous Leaky Gut blog.

If you have any questions regarding the health topics that have been raised, or any other health matters please do contact me (Amanda) by phone or email at any time.

amanda@cytoplan.co.uk, clare@cytoplan.co.uk, 01684 310099

Amanda Williams and the Cytoplan Editorial Team: Joseph Forsyth, Simon Holdcroft and Clare Daley

Last updated on 27th January 2016 by cytoffice


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