Do I really need to cut out gluten?

16 Jul

The question everyone with an autoimmune condition is asking (and my honest answer)

If you have an autoimmune condition, the chances are someone has told you to cut out gluten. Maybe it was a blog post, a well-meaning friend, a health practitioner, or one of those very thorough autoimmune protocol books that arrived on your doorstep after a late-night internet spiral. If you haven’t cut it out yet, you’ve probably been told you absolutely should. Or, alternatively, a medical professional may have looked at you blankly when you mentioned it and said there was no need unless you had coeliac disease.

So which is it?

By the end of this post, you’ll understand why the answer is more nuanced than either camp tends to admit, when removing gluten genuinely matters, which autoimmune conditions carry the highest risk, and what happens in your gut every single time you eat gluten (yes, everyone’s gut, not just the sensitive ones). No gatekeeping, no blanket rules, no guilt. Just the biology, explained clearly, so you can make an informed decision for your own body.

The noise out there is exhausting

If you’re living with an autoimmune condition, you are probably no stranger to the dietary advice merry-go-round. You’ve been told to cut this out, add that in, try this protocol, ditch that food group. Gluten is almost always somewhere near the top of the list. The problem is that the advice tends to arrive at one extreme or the other. Either gluten is the root of all autoimmune evil and you must eliminate it immediately and forever, or it’s a wellness industry myth and you’re fine unless a biopsy says otherwise.

Neither of those positions serves you particularly well.

What I want to do here is give you a middle ground that’s actually grounded in the science and clinical experience. Whether gluten is a significant problem for you depends on several specific factors: your diagnosis, your current immune and health status, how sensitive you are as an individual and, importantly, whether you’ve actually been tested for coeliac disease (more on that in a moment, because this matters more than most people realise).

If autoimmune disease or immune-related conditions are new terms for you, you may want to read this article: Autoimmune Disease Explained.

A client who couldn’t wait

Before we get into the details, let me tell you about a client who got in touch before we’d even had our first appointment together. She was in such acute abdominal pain that she asked whether there was anything safe she could do while waiting for her first appointment and without having had a full assessment. The one thing I suggested, because it was simple, low risk and very relevant, was to remove gluten from her diet. Whole food gluten replacement, not a trolley full of gluten-free biscuits (we’ll come back to that distinction another time).

Within a few weeks by the time of her initial appointment, the pain had already significantly reduced and visits to the toilet had normalised.

Now, this wasn’t a diagnosed coeliac case (both blood test and biopsy were negative). It wasn’t even a confirmed gluten sensitivity. But reducing one of the most inflammatory and immunologically active proteins in her diet had taken away an aggravating factor, and her gut had started to settle and heal. Whether gluten needs to come out of her diet permanently is something we’re still working through and further tests will let us know. But in that active, symptomatic period, it made a tangible difference.

That’s the principle I want you to hold on to as you read the rest of this.

Why gluten is a bit of a handful for the immune system

Here’s something that doesn’t get explained particularly well. Plants evolved proteins like gluten to help protect the seed from predators and give it strength and energy. It’s one of the reasons bread dough stretches and traps air so beautifully and it is the main protein source in bread. Unfortunately, the same characteristics that make gluten brilliant for protecting seeds and baking also make it unusually difficult for our digestive system to completely dismantle.

Gluten is not a straightforward protein. It’s a large, complex molecule made up of two main protein fractions (gliadin and glutenin), and the bonds that hold it together are unusually resistant to being fully broken down during digestion. Most food proteins get dismantled pretty well in your gut after eating. Gluten doesn’t. Some of the larger gluten fragments that are left behind are unusual enough that your immune system pays far more attention to them than it does to most food proteins.

This matters because it means that even before any question of sensitivity or diagnosis, gluten places a higher immunological demand on the gut than most other food proteins. The issue is that gluten is harder to process, and what’s left behind after digestion is recognisable to the immune system in ways that, for some people, can set off a cascade of inflammation - this is the part that’s worth understanding.

What actually happens when you eat gluten

Imagine your gut lining as airport security. Every day it’s making thousands of decisions about what can safely pass through into your bloodstream and what needs to stay behind. Most of the time it’s remarkably good at its job and we don’t even think about it.

Now imagine one passenger arrives mid summer, wearing a huge shaggy coat, carrying six pieces of oversized luggage and behaving differently enough to catch the attention of the security guards. That’s a bit like gluten, let’s think of her as our demanding diva.

Remember that gluten is unusually difficult to break down. Most proteins arrive at security neatly unpacked. Gluten doesn’t. Our diva insists on dragging several oversized bags with her, representing the larger protein fragments that digestion hasn’t fully broken down.

But she has another trick up her sleeve…

Research has identified a molecule called zonulin, which acts rather like the security guard controlling the gates between your gut and your bloodstream. One of gluten’s main protein components (gliadin) triggers the release of zonulin, opening the gut lining. In effect, our demanding diva, gluten, triggers security to open the gates just a little wider than usual, allowing her, and those oversized bags, through into your bloodstream.

Gluten the diva at airport security gates

Here’s the really interesting part…

This isn’t something that only happens in people with coeliac disease or gluten sensitivity.

Research shows that gluten increases intestinal permeability in everyone to some degree. [1] The difference isn’t whether the gate opens, it’s in how the immune system responds to what walks through it and intestinal permeability is one part of a bigger picture I refer to as the autoimmune triad.

If you’re living with an autoimmune condition, your immune system is already operating on higher alert. So when the diva in the shaggy coat strolls through security dragging six oversized bags behind her, she attracts far more attention than she otherwise would. That’s when the protest begins and because the immune system works throughout the whole body, that protest doesn’t just stay in the gut. It can show up in your joints, your brain, your skin or your energy levels (read on for more on this). If your immune system is calm and well regulated, those gluten fragments are usually dealt with without much fuss.

This doesn’t mean gluten is inherently dangerous for a calm, well-regulated immune system, it means the stakes are very different when yours isn’t. That’s why nutrition is never just about the food on your plate, it’s about the bodily environment it lands in and the state of the immune system that’s receiving and interpreting those food messages.

(There’s more to the structural picture of ‘leaky gut’ here, including the proteins that work alongside zonulin in maintaining gut barrier integrity, but that deserves its own article. Keep an eye out for that one.)

The conditions where gluten deserves particular attention

Not all autoimmune conditions have the same relationship with gluten, and this is where the “it depends” answer becomes useful, rather than annoying.

Coeliac disease

Before we get into which conditions matter most, a piece of context that tends to surprise people. Coeliac disease is often described as the tip of the iceberg, and the analogy comes from the fact that studies show that for every diagnosed case of coeliac disease there may be somewhere between 3 and 7 undiagnosed cases sitting in the general population, going about their lives with symptoms nobody has yet connected back to gluten. That’s around up to 85% of cases undiagnosed! [2] The clinical picture has shifted too. What used to be called the “classical” presentation (chronic diarrhoea, weight loss, obvious malabsorption) is now seen in the minority of coeliac cases. The majority of people with coeliac disease today present without those textbook gut symptoms,and much of what shows up instead is happening elsewhere in the body entirely, affecting almost every other organ system. So the idea that you would know if gluten was a problem for you, because you would be doubled over after a slice of bread, is one of the least helpful assumptions circulating in nutrition circles. As a result coeliac disease is now categorised as a “systemic autoimmune disorder” and not just digestive autoimmunity.

Hashimoto's thyroiditis

Is probably the most well-known example of where gluten deserves particular attention. The connection works through a mechanism most commonly described as antibody cross-reactivity. The gliadin protein in gluten shares structural similarities with several tissues in the body, including thyroid tissue proteins such as thyroglobulin. When gliadin proteins cross the gut lining and encounter a primed immune system, the antibodies produced against gliadin can end up cross-reacting with thyroid tissue. In simple terms, the immune system, having learned to attack gliadin, mistakes part of your thyroid for the same threat and goes after it too. [3] A 2023 meta-analysis found that a gluten-free diet was associated with a meaningful reduction in thyroid peroxidase (TPO) antibodies in people with Hashimoto’s, even without a coeliac diagnosis. [4]

It’s worth knowing that this cross-reactivity phenomenon isn’t limited to thyroid tissue. Gliadin has been shown to cross-react with proteins in multiple neurological tissues, the liver, the pancreas, the adrenal cortex, ovarian and testicular tissue and even bone cells. This is part of why gluten-related immune activity can show up in so many different places, and why the “just a gut issue” framing is now outdated. Cross-reactivity can often show up with viruses such as EBV too.

This is also where the NICE guidelines are worth paying attention to. NICE recommends that all people diagnosed with autoimmune thyroid disease (including Hashimoto’s) and Type 1 Diabetes are offered serological testing for coeliac disease at the point of diagnosis. [5] This is a piece of information that a significant number of people with autoimmune conditions have never been given. If you have Hashimoto’s or Type 1 Diabetes and you've never been tested for coeliac disease, that test is something you can ask your GP for directly.

One quick practical note while we're here. Coeliac blood tests rely mainly on IgA antibodies, and roughly 2-3% of people with coeliac disease have selective IgA deficiency (a 10-15x higher rate than in the general population). If your total IgA isn’t checked alongside the coeliac antibodies, a low IgA can produce a falsely reassuring negative result, so ensure that total IgA is included in the request. [6]

Beyond Hashimoto’s and Type 1 Diabetes, coeliac disease is associated with a much wider range of autoimmune conditions than most people appreciate, and the risk goes in both directions - having coeliac disease increases the risk of developing another autoimmune condition, and having another autoimmune condition raises the likelihood of coeliac disease being in the picture. I'll be writing a separate piece on this soon, because the story it tells about how the immune system tends to widen its net is important and it deserves proper air time.

For now, the shorter version. If you have any autoimmune diagnosis, gluten is worth taking seriously as a potential factor, not just the conditions with the most obvious link. Non-coeliac gluten sensitivity (NCGS) also sits on this spectrum. It’s not coeliac disease (there’s no damage to the villi in the small intestine and the standard coeliac antibodies may be absent), but the immune response to gluten is real, the symptoms are real, and the inflammatory signal is measurable. NCGS is more common than coeliac disease and remains significantly underrecognised.

Gluten doesn't just stay in the gut

Sign saying 'Your gut in not Las Vegas — *Attributed to Dr. Alessio Fasano.*

Here’s something that surprises almost everyone. When people think about gluten and health problems, they think digestive symptoms…. bloating, diarrhoea, abdominal pain. While those are real and common, they’re far from the whole picture. Some of the most significant manifestations of gluten-related immune activity have Nothing to do with the Gut. At. All.

The immune system is a body-wide system. When it generates antibodies in response to gluten, those antibodies don’t politely just stay in your digestive tract. They circulate across your WHOLE body. In people with existing autoimmune activity or gluten sensitivity, that body-wide immune response can show up in places that seem completely unrelated to what you're eating.

The brain is a significant example of this

Research has identified something called gluten ataxia, where circulating anti-gliadin antibodies target tissue in the part of the brain that affects balance and coordination (the cerebellum). [7] Peripheral neuropathy (nerve pain and numbness) is another recognised neurological manifestation of gluten-related immune activity. [8] Beyond these more defined presentations, the broader gluten-brain connection is increasingly well documented. Depression, significant mood disruption and cognitive difficulties have all been associated with gluten exposure in people with coeliac disease and NCGS alike, driven by systemic inflammation, gut-brain axis signalling and direct neuroinflammatory effects. [9] If you have ever noticed your mood take a meaningful dip after a period of eating more gluten, this is the biology that might explain it.

Joint symptoms are another area worth naming. People with inflammatory joint conditions, including rheumatoid arthritis and spondyloarthropathy, frequently report that gluten aggravates their symptoms. I am one of these people, who despite being happily in remission, will know about it in my joints if the lure of a good French boulangerie gets too much while on holiday. Increased intestinal permeability allows pro-inflammatory molecules into the bloodstream, and an activated immune system is well placed to direct that inflammation towards the joints. [10] People with rheumatoid arthritis have been found to carry elevated anti-gluten antibodies at higher rates than the general population too, suggesting an active immune response to gluten in at least a subset of this group. [11]

The point is not that gluten causes all of these conditions. It’s that if you have autoimmune activity and you’re experiencing symptoms that seem distant from the gut (brain fog, low mood, nerve symptoms or joint pain that flares and settles unpredictably), gluten’s systemic effects are worth factoring into your individual picture. It is not only a digestive question and working on lowering inflammation across the body is essential.

“That gluten sensitivity is regarded as principally a disease of the small bowel is a historical misconception”

— M. Hadjivassiliou. J Neurol Neurosurg Psychiatry. 2002

The flare rule

Whatever your baseline position on gluten, there is one situation where I think the answer becomes much clearer. During any period of active immune activation or flare, where your symptoms are presenting or you’re generally more fatigued and in pain - take gluten out.

When the immune system is already in a state of heightened reactivity, introducing an immunologically demanding molecule that opens the gut lining, enters the bloodstream and can provoke cross-reactive antibodies is simply adding fuel to a fire that is already burning out of control. Said without blame or judgement, it just makes a lot of sense to remove an aggravating factor when the stakes are higher.

During any kind of autoimmune flare, take gluten out.

You don’t have to commit to forever. You don’t have to overhaul your entire kitchen in a single weekend and I’ll go into timing in a separate article. But during active periods of immune activity, whole food gluten replacement is one of the lowest-risk, highest-potential-return steps you can take. This isn’t just a case of loading up on things from the gluten-free aisle though, but trying to include as many real whole foods as possible instead and limiting processed gluten replacements which can cause just as many issues due to the collection of additives.

If you want a fuller list of what to prioritise and what to limit during a flare, I've written about this here.

In summary

Gluten is a structurally complex protein that has been shown to trigger increased gut permeability in everyone (via the release of a molecule called zonulin). Whether that matters specifically for you depends on your immune status, your diagnosis and your individual sensitivity.

People with Hashimoto’s thyroiditis have particular reason to take gluten seriously, because of the antibody cross-reactivity between gliadin and thyroid tissue. NICE guidelines recommend coeliac testing at diagnosis for autoimmune thyroid conditions and type 1 diabetes. If you have either of these diagnoses and you’ve never been offered that test, ask for it (and ask for total IgA to be checked alongside, it can be done as part of the same blood test). Gluten is also worth taking seriously for a much wider range of autoimmune conditions than the obvious two - separate article coming on that soon.

Gluten’s effects are not limited to the digestive system. Circulating antibodies can act body-wide, and gluten-related immune activity has been associated with neurological symptoms (including ataxia, peripheral neuropathy and depression), as well as joint inflammation. If your symptoms include brain fog, low mood or joint pain that seems disconnected from anything obvious, this is worth factoring in.

During any active flare or period of heightened immune activity, removing gluten is a straightforward, low-risk step worth taking regardless of where you sit on the spectrum.

What next?

If reading this has made you realise you’ve never been tested for coeliac disease despite having an autoimmune diagnosis or some of the other symptoms mentioned above, that’s your first step. Ask your GP for the relevant serological testing, and make sure you're still eating gluten for at least 6 weeks before you go (I know, this is a real downside unfortunately), because a gluten-free diet before testing can produce a false negative. Ask specifically for total IgA to be checked alongside the coeliac antibodies. If your test comes back negative but your symptoms and family history still point strongly towards gluten being a factor, know that a small percentage (around 3-5%) of people with coeliac disease are seronegative (i.e. the standard antibody tests don't pick them up), so a negative result isn't always the final word.[12] That's a conversation worth having with a practitioner like me who can look at the wider picture and do genetic testing too.

If you’re in an active flare (highly symptomatic) and haven’t yet removed gluten, now is the time to start, and do it properly. There’s a separate article coming shortly on exactly how to go gluten-free (what actually counts, how long to give it, and why processed gluten-free products are not necessarily the answer), so if that’s where you're heading next, keep an eye out.

If you’ve been going around in circles with your symptoms, trying things, removed gluten but not feeling any different (the next article will answer this specifically), feeling confused by the contradictory advice and not sure where the real levers are in your own health, that’s exactly what I’m here to help you with. Book a call and let's have a proper conversation about what’s actually going on for you and where to start.

Click here to book in for a chat

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