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An Autoimmune Protocol

This article discusses the Functional Medicine approach to autoimmune conditions as set out in Tom O' Bryan's book The Autoimmune Fix. As he explains in his book, the starting place for all nutritional therapists, when addressing autoimmune disease, is with the food you eat, removing the foods that are a major source of inflammation. Gluten, dairy, grains, processed sugar and flour, beans and poor quality vegetable oils are often triggers for autoimmunity. Clearing these foods out the diet for 10 days (or longer if necessary), can help to reset a person's system. It is important to remember that everyone is different and that a nutritional therapist will create a personalised protocol based on testing and consultations. Please use the information in this article as a reference to help you know what to expect from your therapist or healthcare professional.

Removing sugar, dairy and gluten from the diet is often the first step, due to the inflammatory nature of these foods. This will allow the digestive and immune systems to calm down, heal and reset. Reducing inflammation is like ceasing to pour gasoline on a fire - one still has to put out the fire. This is achieved by rebuilding the damaged tissue to create a better, healthier intestinal environment for good bacterial growth, and to heal a leaky gut. The aim of an autoimmune diet is to foster an eating style that favours foods and nutrients which calm down inflammation and reverse the autoimmune cascade. The diet normally consists of two phases. Phase 1 is an elimination phase, which eliminates the three primary triggers, gluten, sugar and dairy, for three weeks.

Most people feel significantly better and notice symptom reversal during this phase. During this phase you can eat:

All forms of fruit and vegetables and nuts (other than peanuts). Frozen are acceptable, preferably organic and locally sourced where possible. Avoid canned fruits and veg and those preserved with sugar or salt.

The following foods are anti-inflammatory and known to help heal the gut:

  • Cinnamon (1/10th tsp daily)

  • Cruciferous vegetables (broccoli, cauliflower, Brussel sprouts, cabbage, bok choy) contain a family of vital nutrients called glucosinolates that are potent polyphenols particularly useful for lowering inflammation in the intestines

  • Dark coloured fruits such as berries, cherries, red grapes

  • Green tea (1-3 cups per day) which is also a prebiotic

  • Omega-3 fatty acids must be acquired through diet or supplement as the body cannot make them. Amongst numerous other benefits, they turn on genes that lower inflammation in the gut. Vegetarian foods high in Omega-3’s include black walnuts, pecans, pine nuts, chia seeds, flaxseeds, basil, oregano, cloves, marjoram and tarragon

  • Parsley

  • Tomato juice (140ml)

Inulin is an excellent prebiotic. Most people get 70% of their inulin from wheat. If you don't get enough inulin, any good bacteria in your gut that is inulin-dependent will starve. It is therefore important to make sure you include inulin-rich foods as part of your daily diet when cutting gluten and wheat from the diet. Chicory root contains the highest concentration of inulin. Other inulin rich foods include leeks, asparagus, artichokes, onions, garlic, dandelion root, bananas and plantains. If any of these foods cause you bloating, abdominal cramping, loose stools, gas etc it is often an indication of SIBO, and I would recommend the SIBO breath test to check.


While fruits are not excluded in an autoimmune diet, they can be very high in sugar, which may have a detrimental effect on your blood sugar levels. Wherever possible, favour low-sugar fruits, such as:

  • Apricots

  • Plums

  • Apples

  • Peaches

  • Pears

  • Cherries

  • Berries

Other fruits to include in moderation are:

  • Acai berries

  • Apricot

  • Avocado

  • Banana

  • Blackberries

  • Boysenberries

  • Cantaloupe

  • Cherries

  • Coconut

  • Cranberries

  • Fig

  • Goji berries

  • Grapefruit

  • Guava

  • Honeydew

  • Huckleberries

  • Juniper berries

  • Kiwi Fruit

  • Kumquat

  • Lemon

  • Lime

  • Lychee

  • Mango

  • Nectarine

  • Olive

  • Orange

  • Papaya

  • Passion fruit

  • Peach

  • Pear

  • Persimmon

  • Pineapple

  • Plum

  • Pomegranate

  • Pomelo

  • Quince

  • Star fruit

  • Strawberries

  • Watermelon

Nuts and Seeds

Nuts and seeds are an excellent source of protein. Nut based flours and nut butters are a good way to get nut protein, although be on the look out for varieties that contain processed ingredients. Try to avoid sugary nut-bars and favour activated nuts as the phytic acid in nuts can be a problem. It is possible to buy activated nuts in the UK, but you can activate nuts yourself by soaking overnight in warm salty water, then roasting until dry and crunchy.

Good seeds and nut choices include:

  • Almonds

  • Australian nuts

  • Beech

  • Brazil nut

  • Butternut

  • Cashew

  • Chestnut

  • Chia seeds

  • Chinese almonds

  • Chinese chestnuts

  • Filbert

  • Flax Seeds

  • Hazelnut

  • Hemp seeds

  • Indian beech

  • Kola nut

  • Macadamia

  • Pecan

  • Pine nuts

  • Pistachio

  • Poppy seeds

  • Pumpkin seeds

  • Safflower


Vegetables are extremely adaptable and generally lower in sugar than fruit. The best way to eat vegetables is in their raw form, but steaming, roasting and baking are also good options. You can add them to soups, chillies, stews, roasts, stir-fries and casseroles. I advise you to pack in as many vegetables each day as possible, using a wide variety of different colours. Any vegetables are allowed in phase 1 as long as you do not have an allergy, except soy or corn as these can be genetically modified and lead to leaky gut.

Good vegetables include:

  • Artichoke, globe

  • Artichoke, hearts

  • Artichoke, Jerusalem

  • Arugula

  • Asparagus

  • Avocado

  • Beans (all varieties)

  • Beetroot and beetroot greens

  • Bok choy

  • Broccoli

  • Brussel sprouts

  • Broccoli

  • Cabbage

  • Carrots

  • Cauliflower

  • Celery

  • Collard greens

  • Corn – organic only

  • Cucumbers

  • Aubergine

  • Fennel

  • Garlic

  • Jicama

  • Kale

  • Leeks

  • Lettuce

  • Mushrooms

  • Mustard greens

  • Onions

  • Parsnips

  • Peas

  • Peppers

  • Potatoes

  • Pumpkin

  • Radishes

  • Rhubarb

  • Romaine lettuce

  • Rutabaga

  • Sea vegetables

  • Shallots

  • Soy (edamame, tofu, etc – organic only)

  • Spinach

  • Squash

  • Sugar snap peas

  • Sweet potato

  • Swiss chard

  • Tomatoes

  • Turnips and turnip greens

  • Watercress

  • Courgette

Animal protein and fish

Organic grass-fed animal protein to avoid antibiotic and hormones given to non-organic. Salmon should be organic or wild Alaskan. Tuna is often high in mercury, so favour smaller fish such as sardines or anchovies.

Healthy fats

Coconut oil, coconut butter, coconut milk and coconut cream are loaded with healthy fats. Coconut’s creamy texture is great for dairy-free cooking. Because of its high fat content, coconut can be used as a dairy substitute in most recipes, although it does have a distinctive taste so be mindful of whether it will complement your meal. The best options for cooking oils are clearly labelled as extra-virgin or cold pressed. When using oils in cooking make sure you do not heat to smoking levels. When oils begin to smoke, they are becoming oxidised and produce high amounts of free radicals.

Oils with high smoking points include:

  • Avocado oil

  • Coconut oil

  • Ghee

  • Macadamia oil

  • Olive oil

Baking flour

These flours are all fine as long as they are gluten-free with no added sugar or additives:

  • Amaranth flour

  • Arrowroot flour

  • Bean flour

  • Brown rice flour

  • Buckwheat

  • Corn flour or meal

  • Millet flour

  • Plantain flour

  • Potato flour and starch

  • Quinoa flour

  • Sweet potato flour

  • Sweet rice flour

  • Tapioca starch

Fermented foods

Adding fermented foods is a great way of rebuilding and maintaining a healthy gut. Some people start very slowly, simply having 1 or 2 teaspoons of the juice – for example buying bottled kimchi, sauerkraut etc and having a tsp of the juice. Build up slowly to a forkful of fermented vegetables every day. These foods themselves supply and produce probiotic bacteria that are then introduced into your digestive tract. It may be worth making your own at home as the commercial ones such as sauerkraut often have sodium benzoate which stops the fermentation, as well as added sugars and other additives.

Good choices include:

  • Coconut kefir

  • Naturally fermented pickles (as opposed to pickles made from malt vinegar which contains gluten)

  • Kimchi

  • Kombucha

  • Olives

  • Pickled ginger

  • Sauerkraut

Getting rid of gluten

Going gluten free means getting rid of gluten completely. Avoiding processed foods makes your chances of avoiding gluten so much better. The best way to eat during the next 3 weeks is preparing food using ingredients as they appear in nature, like fresh fruits and vegetables. When in doubt simply Google the name of a product or ingredient asking whether it is gluten free. I would also suggest buying the book Autoimmune Fix – Tom O’ Bryan – which I use as a guideline.

General guidelines

Choose organic as much as possible. The amount of pesticides, herbicides, fungicides, glyphosate etc being sprayed on the food, is harmful to our gut and overall health. This is also why I recommend IONGUT as a supplement, to help heal the gut. If you cannot choose organic, check the list of the Clean 15 foods which are not high in chemicals and are safer to eat even though not organic, and The Dirty Dozen which should only be eaten if organic.

Going gluten, dairy and processed sugar free is all or nothing for results. Little mistakes or cheats can sabotage your chances of feeling better as it takes only the tiniest speck of gluten, sugar or dairy to keep the immune system on red alert and the inflammation raging. Less that 1/8th a thumbnail of gluten can activate the inflammatory cascade to last 2-6 months. Imagine what is happening when you are eating these products more than once a day.

By taking care of leaky gut, you reduce the amount of toxic bacteria and food particles that pass through the gut lining into the body, causing an inflammatory immune response. The fastest growing cells in the body make up the inside lining of the intestines. That’s why it takes only 3 weeks to start seeing improvements.

Nutrients to reduce autoimmunity

Autoimmunity and inflammation are caused by a dysregulated and over-active immune system. To address this the immune system needs to be balanced, not boosted. If you are in severe, crippling pain, or a cascade of autoimmune disorders, the standard pharmaceutical approach for dealing with autoimmune diseases is to suppress the immune system entirely. These powerful medications may be helpful in the short-term. However, in the long term they may affect other tissues in the body; they suppress the immune system so completely that it often cannot protect you when other triggers or irritants come your way and even increase gluten and other food intolerances leading to the development of certain other autoimmune diseases.

Anti-inflammatory nutrients

First and most importantly is to eat the highest quality of food, preferably organic. Second, supplement with the right nutrients.

Aim of protocol

  1. Stop the production of antibodies. This involves finding and removing the triggers of the disease such as microbes and allergens (including food).

  2. Calm down the inflammatory cascade

  3. Activate anti-inflammatory genes

  4. Stimulate healing

In the spectrum of autoimmune development there are years of tissues destruction with no symptoms. In autoimmune tissue regeneration, there is a spectrum of healing that takes time. It takes 6 months to a year to see noticeable improvements in laboratory testing. There will be a recommended protocol to repair a 'leaky gut,' probiotics to replenish gut flora and nutritional herbs and supplements to help with repair and healing. If after following Phase I for 3-4 weeks, a person does not notice a discernible improvement in symptoms, it may be necessary to consult a practitioner to find out what other culprits may be involved (bacteria, viruses, toxins, chemicals etc.) and whether there are additional worrisome foods which need to be avoided.

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