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Food Intolerance Testing: Want to Find Out Your Autoimmune Food Triggers?

by | Oct 6, 2022 | Autoimmune, Autoimmune Disease, Food Sensitivities / Testing, Home/Blog, Nutrition, Nutrition

What foods, if any, should be eliminated when you have autoimmunity is probably the number one most discussed subject.

When you are first diagnosed or when you first start Googling and thinking about what you might change, there are many many (MANY!) differing opinions and considerations and it can be very hard to work out for yourself if food is causing or contributing to your symptoms, and if so which food/s???

Some of the autoimmune diets cut out large numbers of foods and food groups because they *may* cause problems for *some* people with autoimmune disease, with the thinking being that in the early days at least it’s better to err on the side of caution and try and bring inflammation down quickly. As with everything with autoimmune disease, there is no correct approach for everybody, the highly restrictive autoimmune diets can be a great tool for some people and provide quick wins although I feel it’s very important to understand that this level of restriction needs to be short term only and used as a tool to better understand the individual’s landscape.

But in my clinical practice, if it’s appropriate, I sometimes choose to use food reactivity testing rather than broad eliminations to gauge an individual’s immune relationship with food.

What’s the Connection Between Food Intolerance and Autoimmune Disease?

Both food intolerance and autoimmune disease happen when your immune system loses the ability to understand what to tolerate and what to attack. This is called loss of immune tolerance. When your immune system is reacting to food, it’s loss of dietary protein tolerance, when your immune system is attacking your body, it’s loss of self-tolerance and these immune mechanisms are related to each other and so they often co-occur in a person with autoimmune disease.

Just remember – autoimmunity is never always anything, so you can absolutely have an autoimmune disease and have excellent dietary protein tolerance! The trick is to work out YOUR specific situation and not make assumptions either way.

If you are having immune reactions to food, this can be directly triggering autoimmune disease in some people, or just throwing fuel on the fire of inflammation in other people. The inflammation and immune response to these foods can have local, gut consequences or inflammatory effects anywhere in the brain or the rest of the body.

Some of the symptoms of these immune-mediated food reactions include:


Join, muscle or nerve pain

Hair loss

Difficulty concentrating or Brain Fog

headaches or migraines

Skin rashes

Autoimmune flares of any kind

But there may also be silent consequences such as damage done to the gut wall, changes to the healthy balance of bacteria in the body, increased susceptibility to infections or poor recovery from infections, poor wound healing or injury recovery and significant increases in inflammation in the body.

And for some people food reactions can be directly triggering their autoimmunity, and I’ll discuss more about the mechanism for this in another article.

Which Foods Are The Problem?

There are some foods that are The Usual Suspects. You will all have heard discussions about gluten and dairy in the context of autoimmunity. But I think it’s important to understand that your immune system can react to ANY food, especially if you have an autoimmune disease, a chronic infection such as Epstein Barr virus, taking long term medication that affects the gut, or if you have had a mould exposure.

So one of the reasons that I think food reactivity testing can be so useful for people with Autoimmune disease is because what if you are having a strong immune reaction to turmeric, or avocados or gelatin – all foods not just found on healing and anti-inflammatory diets, but encouraged and often eaten daily in large amounts.

Or, if you are on the gluten free diet and reacting to potato, tapioca and yeast – all found liberally in LOADS of gluten free processed foods.

In both of these scenarios

If you have a food intolerance, your immune cells have decided that a particular protein or food molecule is a threat. While it’s not as simple as your allergy being a direct trigger for your autoimmune disease, it can contribute – alongside stress, poor sleep, impacted gut health, prior sickness, and many other factors.

When you develop a food intolerance, it causes problems for your gut. First, the localised inflammation caused by your immune system interferes with the health of your gut mucosa. Which leads to an imbalance in your microbiome, and a higher likelihood of leaky gut.

When leaky gut is in full effect, small particles of food – including the allergens – begin to move around the bloodstream. These allergens can wind up in different parts of the body, causing your immune system to ramp up and start attacking your healthy tissue – through a process called [molecular mimicry]. A cycle begins where attacking healthy tissue causes more inflammation, more symptoms, and more pain.

And autoimmunity in turn can create new food intolerances, causing a loss of [oral tolerance]. It may feel like you don’t know where to begin when dealing with your food issues and autoimmune disease. Mealtimes can feel fraught, or end up incredibly samey. In order to have any chance of tackling your diet alongside autoimmune disease, it’s important to understand: What foods may be causing issues?

Why Do Certain Foods Make My Autoimmune Disease Worse?

While some foods are known to be inflammatory, ​​there’s a wide range of additional foods with the potential to cause your symptoms to flare up. So while this is by no means a comprehensive list, it should provide a starting point for you to consider what may contribute to your autoimmunity.

Common food intolerances include:

  • Gluten – The mechanism behind gluten sensitivity isn’t fully understood. Genetic mutations, and environmental factors can contribute to Coeliac disease, but gluten sensitivity may be caused by a change of gene expression in your gut mucosa. It can be stealthy too – gluten intolerance can develop in the innate immune system of your gut, not alerting your main immune system until damage has already been done to your gut wall.
  • Dairy – Your body can develop an intolerance to cow’s milk in several ways: through existing damage to your gut affecting your production of the enzyme that breaks down lactose, trying it after a long time not consuming dairy (loss of oral tolerance), and outright dairy allergy where your immune system sees the proteins in milk as a threat.
  • Soy, egg, nuts, seeds, fish, shellfish, and corn – Common allergens that are often hidden in ready-made foods, soy sensitivity can occur at any point when your immune system perceives certain proteins as a threat.
  • Beans and other food containing lectins – Lectins like to clump together in your gut and bind with carbohydrates. This makes them impossible to break down, and causes gastrointestinal symptoms, before contributing to inflammation and autoimmunity.
  • Nightshades – A family of vegetables that contain alkaloids, a natural defence mechanism that can disrupt your gut health and cause inflammation.
  • Histamines – a neurotransmitter that triggers [inflammation].
  • Artificial food colouring and flavours – These hidden ingredients are made up of haptens, a toxin that’s smaller than the proteins of your body, or the other food molecules you eat. Haptens can slip through the gut wall a lot easier, and when they attach to your tissue they register as a threat, causing autoimmunity as your immune cells attack otherwise healthy cells.

You may feel like you’re looking for several needles in a haystack when you start, trying to figure out what foods are contributing to your health issues. But thorough, specialised food sensitivity testing – and someone to go through the results with you – is your secret weapon.

What Does a Food Intolerance Test for Autoimmune Disease Involve?

Functional testing for food intolerances is different from a standard allergy test you may have taken in the past. Food allergy testing for autoimmune disease checks for signs of immune reactivity in relation to sensitivity, instead of simply checking if a reaction exists. When you meet the functional medicine practitioner who orders your tests, they have considered your functional medicine timeline and have really taken the time to get to know you, your symptoms, and your concerns. We don’t assume there’s an “acceptable” range in your test results – we look at your results, and your symptoms as a whole.

There is no definitive list of tests – we decide on a range of trials tailored to you and your symptoms. But the functional immunology and autoimmunity food reactivity tests may include:

  1. Wheat and Gluten proteins – A test that dives down into the many different types of proteins in wheat that can cause an immune system response, looking for 32 different antibodies that indicate a reaction, not just the ones associated with Coeliac disease. 
  2. Wheat and Gluten cross-reactive foods – A clever immune reactivity screening that not only checks if you’re sensitive to cross-reactive foods such as milk, corn, instant coffee, yeast, and other grains, but can check if you have common food sensitivities, or have developed new ones since going gluten-free.
  3. Raw food proteins – Including raw fruit, veg, nuts, seeds, herbs, and fish. It’s important to test for reactivity to foods you can eat raw in contrast with them cooked. For example, raw tomato contains profilins, a potential allergen that is broken down during cooking. The same goes for apples – the protein is broken down and your body no longer recognises it as a threat.
  4. Cooked or combined foods – including commonly cooked fruit, veg, meat, fish, beans, and so on. But also foods that have been prepared in such a way that it changes their proteins or causes cross-reactivity – including cheese, yoghurt, gelatin, tofu, and crab sticks. Ir doesn’t make sense to test foods raw, that you never eat raw – eg chicken or pork. If you only eat it cooked, you should only test it cooked.

The lab needs a sample of your blood to run these tests to look for specific antibodies. Though the list of potential allergens is long, it helps us narrow down the foods that could be causing you discomfort.

How Do I Find Out My Autoimmune Food Triggers?

When you receive your test results we can go through them together, flagging what foods you need to cut out as part of your initial elimination diet. Remember, an elimination diet is only a short-term experiment to check if your food sensitivities are contributing to your autoimmune symptoms. After a few weeks, it’s important to start reintroducing these foods and recording if your symptoms return or worsen, and potentially retesting at the end.

The last thing to understand, is that if your immune system has lost tolerance to a lot of foods, it’s not the food that’s the problem and therefore cutting out foods is not the answer. We will need to dig more to find out WHY your immune system is struggling to tolerate food proteins and address this issue in order to support and calm your immune system upstream.

Adjusting your diet when you have autoimmune disease is a gradual process, so be patient. If you’re feeling lost and need help understanding what changes need to be made, my team and I can be your guide. We cover nutrition in great depth, alongside gut health, stress management, sleep hygiene, infections, mould and toxins in your environment. We specialise in autoimmune disease and food is our primary tool! So working out the right way to eat for YOU is literally our bread and butter and we’d love to help you too.

Click here to learn more or book in to my diary.

You may also like to check out my signature course. The Foundations of Health covers all aspects of gut health, nutrition, detoxification, sleep, and mood, in order to get you feeling more like yourself. 

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Robyn is a Clinical Nutritionist with a specialised interest in the Functional Medicine approach to health. Robyn is very involved with the field of Coeliac Disease, Gluten-Reactive Disorders and Autoimmune Disease. Her passion for the healing power of food, has led her to work with complex cases, involving multiple diagnoses, and chronic health issues such as ME, auto-immune diseases and fibromyalgia. She also has a passion for working with the growing tide of chronic, lifestyle mediated illness; diabetes, cardiovascular disease and obesity, and runs a lifestyle intervention clinic for these issues. Robyn works with patients to nutritionally support their bodies, so that they can heal. She has successfully helped many people around the world improve their health and increase their quality of life. Robyn sees clients in London, Tokyo and New York, and has a virtual practice that allows her to work with people all over the world.

Robyn Puglia

My mission in life is to share my knowledge in order to help people heal. I love to unravel the health stories and the biochemistry to get to the heart of the problem, and to help support nutritional and lifestyle changes that have the ability to transform people’s health. I have seen incredible changes in the health of my clients, and I hope to do the same for you.

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