Years ago, we used to think that autoimmune diseases were just something you had to live with and often medicate for life; there was seemingly nothing to be done about them except manage the condition as best you could. In the last decade or so, we’ve learned that this is, happily, no longer the case.

Clinically, I have even seen the evidence where autoimmune antibodies start reducing, sometimes back into normal, if you do the right things! It won’t always happen, of course, especially with genetic types of AI disease, but I always think if we can at least prevent an autoimmune condition from getting any worse and – importantly – prevent any other developing, we are doing a good job! Autoimmune diseases never tend to come in singles because the process can affect several areas of the body. So, someone may have autoimmune thyroid disease, coeliac disease and lupus, for example, or a common one is diabetes type 1 and coeliac disease. The mechanism is basically the same – and so is the treatment.

Autoimmune disease is a condition really where inflammation combined sometimes with a genetic weakness, an environmental trigger such as a food (gluten especially) or a toxin (mercury, pesticide, mould etc), an infective agent (bacterial, viral etc) and often leaky gut or other body barriers trigger molecular mimicry. This just means the body mixes up things it should be attacking with body tissues with a similar structure and starts attacking that in error. It is an immune system gone awry.

The main thing to remember about autoimmune diseases is that they don’t just come out of nowhere. They take years, sometimes several decades, to develop. The trick I have found clinically is to test early on, especially if there is any risk in the family or symptoms suggest an issue might be developing. More often than  not, though, someone presents to me with an existing autoimmune condition – usually thyroid or coeliac disease – and I then encourage them to check if any others are developing so we can do something about the process and target specific treatment.

a lab icon productsAutoimmune Testing

These are the key areas to test in autoimmunity…you can always read the up to date testing and my thoughts on the various tests etc on the Gluten, Autoimmune and Cyrex tests page here – read the Overview there.

Leaky Gut or Blood-Brain Barrier

First, because molecular mimicry happens very often as the result of a leaky gut or other brain barriers, I would check this. Cyrex 2 will check to see if you are producing antibodies to the gut barrier, but it will also tell us if there are any LPSs – lipopolysaccharides – and those are a really key cause of  continued inflammation in the body. In other words, if those are there, it gives us a clue as to how to treat the inflammatory process, at least in part.

If this is positive, it is likely that something is getting through into the system and triggering the process. You then need to identify what that is and deal with it. It might be foods, toxins, a bacteria, a virus etc.

Similarly, you can test now for a leaky blood-brain barrier using Cyrex 20.

You can also now check for evidence of leaky gut and SIBO in the small intestine. Cyrex 22. This is very different to the breath test in that it is looking for antibodies to bacterial cytotoxins released in SIBO rather than the gases we produce. It also looks for evidence to see if the cytotoxins have caused a leaky gut. You can see more info on this sheet here.

You can read the Overview here and follow the links to find out more about the various Cyrex tests.


To check if autoimmune disease markers are present: I have invented my own ‘general markers’ autoimmunity screen, much cheaper than some of the Cyrex ones to start you off. This is a general ‘can we find evidence easily of autoimmune disease going on?’ test with some specific autoimmune disease types I see a lot included. Use MR1 Autoimmune Screen if it covers what you need. It includes Thyroid Peroxidase, Thyroglobulin Antibodies, Antinuclear Antibodies, Mitochondrial Abs, Smooth Muscle, Gastric Parietal (stomach eg. for acid and intrinsic factor/B12), Reticulin, LKM, Islet Cell (pancreas), Adrenal, Ovarian and Testicular.

Use Cyrex 5 instead for a really comprehensive autoimmune screen (you can see an interpretation table of what each antibody means etc here) or use the specific tests if you are looking for just a couple of things: Cyrex 6 for diabetes, Cyrex 7 or 7X for the neurological autoimmunity screen, Cyrex 8 for joint autoimmunity and Cyrex 20 for blood-brain.

Pathogens and other triggers

Next, consider if pathogens are causing your issues. Cyrex 12 assesses IgG immune reactivity to pathogens that are documented triggers or exacerbators of autoimmunity and chronic disease. The test looks for IgG antibodies to various pathogens including oral pathogens, gastrointestinal parasites, bacterial and stealth pathogens, environmental moulds (molds), viral pathogens and tick-borne pathogens – you can see all of them here. If an IgG antibody is present, it doesn’t show a current infection, but it suggests there is a hidden or latent pathogenic problem that may well be causing you problems or acting as a trigger.

It can also be a good idea to consider levels of known toxic chemicals in your system. Could you have a high levels of something like glyphosate (Round Up) in your system that is triggering cross-reactivity to organs and tissues maybe or messing about with your gut flora, hormones etc? To check that, see the Glyphosate and GPLTOX tests here and maybe also check Cyrex 11 for any clues that you are immunologically reacting to any of the most common ones. In other words, you can now check for presence and immune reaction to them.

Remember you can always read the up to date testing and my thoughts on the various tests etc on the Gluten, Autoimmune and Cyrex tests page here – read the Overview there.


cropped-rx-icon.jpgAutoimmunity Treatment

Autoimmune treatment is a very complex field. In essence, you are trying to restore nutrients, digest better, heal the barriers and lower inflammation as well as encourage regulating T-cells in the immune system to balance the immune system and stop the over-reactivity.

Autoimmune Diet

The first task is to get yourself onto an autoimmune diet. This sounds awful until you see all the tasty recipes I’ve collated for you on the Pinterest AIP Board! Essentially, an AIP (autoimmune protocol) diet is free of grains, dairy, lectins, nightshades, eggs, nuts and seeds and other foods that can trigger autoimmunity, inflammation or allergy reactions. No-one says you have to be on it for life and there are various ‘levels’ of it, but to start your healing off, this is your best approach. Anyway, who wouldn’t want apple plantain fritters, AIP Crusty bread or Cauliflower Spicy Couscous. Here’s a nice Mango and Carob tart to give you hope…!

Paleo and Gluten-Free Vegan Mango Carob Tart {AIP-Friendly, Refined Sugar-Free}

Supplement Protocol

There are certain ‘givens’ for autoimmunity, such as ensuring your Vitamin D levels are optimum (see here for more on that). Don’t believe it necessarily if you’ve been told yours are normal; I would probably see it differently as that factsheet there will tell you!

I am currently building a new Autoimmunity factsheet for you, but for now my advice on autoimmunity, plus a suggested supplement protocol is in the Gluten Plan; I’ve just not had a chance yet to pull it out into a separate factsheet for you, but it’s all there. I’ve included specific products and given dosage ideas etc. Do, of course, be led by your practitioners but please don’t believe there is nothing to be done; there is plenty you can do, trust me!


The Gluten Plan – for details of the different diets you can do and a product-specific protocol to follow. It is heavy on gluten illness – but since gluten is the most common trigger across all autoimmune disease, that’s why I started with it!

My Pinterest AIP Recipe board has over 350 recipes on it to help give you some really tasty, but healing ideas.

There is a great ‘intro’ book by Dr Tom O’Bryan called The Autoimmune Fix. He writes in a very easy to understand manner and all of the basics are there about causes, triggers, diet and supplement ideas. This would be a good book to read to give you a good understanding of what’s going on and what you can do about it.

For all things AIP (Autoimmune Protocol), go here. This is an excellent site full of info and resources you can use. It is a bit US-heavy, but very good.