The Gluten Healing Process

There are three main steps to consider when dealing with a suspected gluten related disorder (a GRD). This is a quick (ha!) introduction to the process we tend to go through. This is discussed in much more depth in the Gluten Plan so do please get that and all will become clear, I promise, but this should start you off:

First: confirm the problem with testing if you can – either off or still on gluten. The most up to date advice is always on this Gluten Testing page here.

Second: establish your healing diet – what do you need to eat or avoid to get well?

Third: take steps to heal any damage done and prevent things getting worse.

grain iconEstablishing your Healing Diet

Most people will start with a Cyrex 3 test if they are still eating gluten or suspect they are still ingesting it. Then, move onto a Cyrex 4 to check for issues with any of the cross-reactive foods or common substitute foods so that they are not ingesting foods the body still reacts to as if they were gluten. They might then want to do a Cyrex 10 which is one of the best antibody food tests I have come across because it looks for food combos, cooked foods, gums etc missed out by other tests. Nothing is 100% as that simply doesn’t exist yet – we don’t know all the mechanisms at play in food sensitivity yet – but we get good and useful results from it.

I hate to tell you, but there is no ‘one diet fits all’ with gluten sensitivity. In fact, I think the traditional gluten free diet has a lot to answer for.

The majority of coeliacs are thought not to heal on a traditional GF diet. There are a few issues with the traditional gluten free diet given for coeliac disease. First, it is only gliadin-free, not actually gluten free. Gliadin 33 mer is the one peptide that has been studied in relation to coeliac disease and, if you have a positive antibody to that, you then go through the coeliac diagnosis process and the treatment given for coeliacs is a gliadin free diet – avoiding wheat, rye and barley which have high levels of it. BUT, many people do not have an antibody to gliadin 33 mer and therefore fall through the diagnostic cracks. There are currently at least 60 different peptides and fractions of grains that can cause problems. What if your problem is with one of those?

The Problem of Cross-Reactive Foods

Additionally, there is a type of gluten in all grains. Sorry to tell you that, but it’s true. Many people who are not healing – and who are even misdiagnosed coeliacs – are not doing so because they are reacting to other fractions in grains. This is most likely because research showsthey cross-react with gluten and have the same effect on the body. In other words, if the food has a similar peptide structure to gluten or wheat etc, and the immune system reacts to it in the same way, you will get the same damage and symptoms as if you had eaten gluten. Not fair, is it?!

Prof Aristo Vojdani,  an immunologist specialising in this area, explains:

 “After establishing the patient on a gluten-free diet, many will return after adhering to this diet for months, and yet they still exhibit the same clinical complaints as they experienced with gluten-containing foods. Undoubtedly, these patients are having reactions to foods which cross-react with gluten antigens.”

“Complete normalization of gut lesions is very rare in adult patients with Celiac disease (8%), despite gluten-free diet compliance. Although a majority (65%) feels better, the ensuing inflammation in the gastrointestinal tract, due to cross-reactions with – and sensitization to – an array of food antigens, remains a cause for clinical concern. 

There are even studies showing how corn and quinoa, to take just two examples, have a similar effect, sometimes worse, on the body as wheat. See these:

Corn Intolerance and

Is Quinoa Gluten Free?

Here is a list of the known (so far) gluten cross-reactive foods and you can check for antibody reactions showing on these foods using the Cyrex 4 test. Try and do this before giving any of them up for maximum info on results.

The Cross-Reactive Foods

If any of these are found positive, they need to be avoided for life in the same way as gluten.





Polish Wheat 






Cow’s Milk 

Alpha-Casein & Beta-Casein 


Milk Butyrophilin 

Whey Protein 


Chocolate (Milk) only milk chocolate is cross-reactive because, obviously, it contains milk. Cocoa itself is safe.

Yeast -a combination of brewer’s and baker’s yeasts is used in tests so could be both or either

So, some people may need to be grain free, not just traditional gluten free (ie. gliadin free) and I think you can see why. It very much depends how far the damage has got, how leaky a person is etc etc. By all means, start with the traditional GF diet, but, if you are not healing, use a grain free one. I invented the TrulyGlutenFree (grain and dairy free) diet to help, plus the Barrier Diet for people with multiple sensitivity, chronic inflammation and autoimmunity. Those are both included in the Gluten Plan for you.

Over the past few years, since I have specialised in gluten sensitivity, and in fact the past 20-odd, where I have specialised in food sensitivity generally, the vast majority of issues raised during healing have come down to someone reacting to something they didn’t know about. Not only is this nasty symptom-wise but it scuppers healing. Exactly what we don’t want.

I can’t give you a standard gluten healing diet: we have found everyone has to find their own way forward. It sucks, I know. Essentially, this step is all about finding where to start and then tweaking your chosen approach to fit what you need. That’s by far the biggest lesson we have learned over the last few years: the traditional gluten free diet is not enough and there is no one diet fits all in GRDs because most have developed other types of sensitivity, largely because of the leaky gut and other body barriers caused by the gluten-zonulin issue.

Barrier  Leaky Gut/Blood-Brain Barriers

Gluten related disorders make you much more likely to increase zonulin production in the body because we know for a fact that gluten upregulates zonulin, so you have much more than normal. Zonulin controls the permeability of your body barriers including the gut, blood-brain, lungs, bladder, skin, eyes etc so making more of it means you are likely more ‘leaky’. This is the main reason why many people with gluten illnesses have multiple food and chemical sensitivities on top of the gluten problem.

Hyper-permeability puts you at risk of peptides getting through into the blood stream and sparking inflammatory, allergenic and autoimmune processes. These can take years to develop and show up as symptoms but the risk is most definitely there. If you have allergies or intolerances, you are already there. In fact, you can read an article I wrote about this here:

Barrier Breakdown: The Cause of Multiple Sensitivity?

So, the first thing you need to establish when thinking about what diet you need to heal properly is how leaky are you? How far has the breach gone? We need a starting point to measure later so that you know when it is OK to start trying new foods.

Cyrex 2 looks for antibodies to the main tight junctions and permeability structures and processes keeping your barriers strong. If they are positive, you are too permeable and the presence of antibodies shows there is an immune process going on. You can then take steps to remove the gluten which is triggering the zonulin and to re-heal the barriers. This is a useful progress test.

You can also check leaky blood-brain barrier with Cyrex 20. This has answered a few questions for people having neurological symptoms (migraine, brain fog, ataxia etc). makes sense for them.

The Right Diet For You

So, your job diet-wise is to use either just the Elimination & Challenge process and/or lab testing combined to find out exactly what your body is up to food-wise. Then, you can make an intelligent and informed decision about the particular type of diet you need, not spend months (more often years) ping-ponging about not really knowing what to eat/what not to eat and whether it’s doing any real good. Once, you have that crucial info, you can design your own diet and use all the fabulous resources around to help you with recipes etc.

Here’s how to use lab testing and elimination & challenge to find your healing diet effectively:

test iconDiet Testing

1. Do Cyrex 4

2. If positive, avoid those foods, using an appropriate diet to help you.

If cross reactive foods antibodies are positive, you need to avoid for life in the same way as gluten.

If common food antibodies are positive, avoid for several months until your Cyrex 2 and/or 20 results are negative.

If any antibodies are negative, that’s a great sign, but do an elimination diet to double-check; your body doesn’t lie and you may not yet be as far on as producing an antibody reaction.

3. If you have already stopped eating one of the common foods and wish to check it, you can do Array 4 and check antibody levels, then eat the food for a month, wait 25 days to allow antibody production enough time and repeat the test. If the antibody to a food has risen, that food is not a good one for you. I wouldn’t recommend doing that with a cross-reactive food though because of the potential for triggering more damage.

4. If you suspect other foods, do the elimination process to identify them, extended antibody testing (Cyrex 10) and non-antibody cellular testing (eg. ALCAT) to try and find them if you need to.

The Different Diets

Obviously, the diet you need will be determined by your earlier tests, either lab or elimination and challenge, preferably both. There are several main diet types you can tap into. Here they are in a sort of ‘food removal’ order for you:

  • Wheat Free (for wheat-sensitives only)
  • Wheat and Dairy Free
  • Traditional Gluten Free
  • Traditional Gluten and Dairy Free
  • Grain and Dairy Free (Truly Gluten Free)
  • Paleo
  • Barrier Diet
  • Autoimmune Protocol (AIP)

Which diet you use will depend on what you need to eliminate, of course.  I have gone through each one with links to resources etc in the Gluten Plan for you. To do that here would take a whole other website! The key message, though, is don’t assume a traditional gluten free diet is enough for you to heal. Because of the leaky body barriers making you more vulnerable to other food and environmental sensitivities and the problem of foods that cross-react with gluten, it probably isn’t. And the statistics suggest that, not just me.

cropped-rx-icon.jpgEstablishing Your Healing Protocol

Now you know the diet you need (or as close to it as you’re going to get), the next thing is to suss out the best supplemental treatment to heal yourself with.

The vast majority of coeliacs, according to statistics, do not heal on a gluten free diet. That’s partly because, with both CD and NCGS, the inflammation, malabsorption and autoimmunity (if triggered) continue for a long time – despite a gluten free diet –  and need to be addressed. The days of just treating with a gluten free diet are over. At least according to lots of experts, including me. We are just waiting for mainstream to catch up 😉

Getting gluten free ‘enough’ is nigh on impossible as we now know that such a tiny amount can trigger a damaging process that lasts a couple of months. So, the emphasis needs to be on healing the barriers to stop anything getting through to the bloodstream in the first place, and calming the inflammation down that is already going on.

What Happens In the Body?

This is an emerging scientific field with a truly fantastic amount of research coming out almost daily. But, this is what we think so far (see following diagram).

To trigger the GRD process, we need:

1. An environmental trigger of some kind (in this case gluten is the main one, but dairy, a fungus, bacteria, stress, trauma, chemical toxin, medicine, drug or virus could be a secondary trigger) plus

2. A genetic susceptibility (the gluten DQ genes, – all of them, not just coeliac DQ2 and DQ8) which leads to

3. An unusually permeable barrier problem. No-one is sure currently whether this always starts with the gut and spreads from there, or can start in the brain and then move onward. Barriers include skin (eg. eczema/dermatitis/psoriasis), lungs (eg. asthma), bladder (eg. interstitial cystitis), blood-brain (eg. migraine, Alzheimer’s, ataxia) and gut. This then leads to

4. Immune dysregulation which causes:

  • food and/or environmental sensitivity because of the breached barriers allowing antigens through
  • inflammation, either systemic (body-wide) or localised (as in the gut, joints, muscles, nerve fibres, fibromyalgia etc) and/or to
  • autoimmunity and molecular mimicry – where the body starts confusing similar-looking food structures for self-antigens of body tissues, glands and cells, as in Hashimoto’s, type 1 diabetes, psoriasis, MS, coeliac disease, parietal cells causing lack of acid and enzymes, adrenal dysfunction, neurological illness etc – could literally be anywhere.

No coincidence then that most gluten sensitives have a problem with poor cognition and memory, neurological issues like anxiety and migraine, muscle and nerve issues, skin diseases like eczema and posriasis, gut symptoms and adrenal/thyroid fatigue Hence it is termed:

A Multi-Organ, Multi-System problem

By Dr Vojdani, Immunologist

The Healing Protocols

In order to heal, you need to address some key factors.

Here is a little summary I saw from Liz Lipski, a US clinical nutritionist, on the Gluten Summit 2014. She says for GRDs, we must:

“repair the leaky barriers, strengthen mucosal immunity, get rid of pathogens like candida and infections, support digestion and absorption specifically the stomach acid, digestive enzymes and bile flow, rebalance the microbiome, lower inflammation and address any other food or chemical sensitivities.”

I would also add dealing with any triggered autoimmunity too.

I was SO glad to hear that because it is really the first time I have heard someone agreeing with what I have been saying now for several years!

I have spent the last few years researching barrier repair and gluten related disorders specifically, and have reviewed zillions of different ideas and supplements. This is the approach I have come up with so far:

supplements iconCore TrulyGlutenFree Protocol

Here, we are trying to do A LOT.  In effect, we need: anti-inflammatories, D3, fatty acids, gut healers, amino acids, antioxidants aimed at detox pathways, anti-virals, immunoglobulins and probiotics.

Unfortunately, if you are grain and dairy free, supplements like that just don’t come easily!  Even if they state gluten free, they will contain other ingredients derived from grains especially corn. Did you know, for example, that 99.9% of Vitamin C is made from corn?! What we have to do is follow the same principles as the core standard protocol above, but do it using separate products a lot of the time.

These are the top three core products I recommend. The rest of the protocol is a kind of ‘pick & mix’ where you choose what products you need as add-ons, depending on what’s going on in your particular case. Please make sure you read the whole Step 3 section in the Gluten Plan for much more about these products, dosages etc and others that you could substitute, plus products for specific issues as below. And always work with your health practitioner!

See Trusted Suppliers for where to get these.

find icon

What Else Might You Need To Address?

Barrier Hyper-Permeability

Check your hyper-permeability levels: if you are too leaky, you will allow food sensitivities, inflammation and autoimmunity to run riot in the future, despite your diet. Do Array 2 (gut) and/or Array 20 (blood-brain barrier), the latter especially if your symptoms are neurological eg. migraine, mood, MS etc. The Arrays 2/20 will act as a starting point and progress marker later for your diet to expand. If anything is positive, treat for barrier healing using the advice in the Gluten Plan. This is not as simple as just taking glutamine, we have found, not least because glutamine feeds candida; good lesson that one! See the Gluten Tests here.


Most gluten sensitives are malabsorbing in some way whether because of villi flattening (coeliac disease), inflammation (NCGS’s) or autommmune processes (eg parietal cells in the stomach) so you need to address your nutrient needs and boost them. Take a good gluten free multivitamin/mineral and some fatty acids as a base (as above). Do any nutrient checks needed, especially red blood cell minerals, Vitamin D, anaemia and osteoporosis bone markers and add anything required using the TGF safe supplements given in the Gluten Plan. Vitamin D and red blood cell magnesium have been especially important for healing we have found clinically so far. Don’t underestimate them. And don’t believe a Vitamin D test result of less than 100nmol/L or 40ug/L is OK for you, it isn’t. I aim for at least 150nmol or 65ug. See Nutrient Tests here. And the bone resorption test here.

Gut Status and Inflammation

Next, check the state of your gut environment (eg bacteria, candida, parasites etc) to make sure you are not harbouring chronic infections that would scupper healing. This is the single biggest area we have found over the last few years that can hinder the healing process. Do the Doctor’s Data Stool Test, which will also give an indication of digestive ability and gut inflammation. It is also a good idea to check whole body levels of inflammation, so ask your doctor to test your ESR and CRP levels or ask me to do it. If anything is positive do an appropriate gut detox or the TGF Candida Plan with or without the diet, depending on whether yeast shows up or not, and use a natural anti-inflammatory using the choices given in the Gluten Plan. Viruses can also be a trigger and need addressing, so don’t forget those either. So-called benign ones rarely actually are. Read more in the Gluten Plan about which viruses to check, how and which infectious nasties we already know can cross-react with gluten, for example.Virus tests are here.


Finally, but possibly most importantly for your future health, you need to look for any autoimmunity processes going on: do Array 5 or the MR1 to look for predictive antibodies to several organs and glands including thyroid, adrenals, intrinsic factor, parietal cells etc. If anything positive is found, treat for auto-immunity using the extended section on this in the Gluten Plan.

There are tons of other issues we could go through, including methylation difficulties, poor liver detox, adrenal and thyroid status etc, but these are some really key ones. There is much more on these and other specific issues in the Gluten Plan.