Hidden signs of coeliac disease in autoimmunity

I’ve worked with many clients, especially those with autoimmune conditions, who are told everything looks “normal.” Their coeliac screen comes back negative, and they’re sent on their way. But for those of us living with complex, chronic illness, the story isn’t always so simple.

Personally, even after a negative result on coeliac testing, I’ve continued to suspect a link between gluten and my immune symptoms, including my history of alopecia areata. The more I’ve learned – through my own experience, clinical work, and research – the more I believe that the conventional approach to diagnosing coeliac disease can sometimes miss the bigger picture.

Here’s why I think that matters.

Coeliac disease presents in different ways

Classic coeliac disease is defined as an autoimmune condition triggered by gluten (a protein found in wheat, rye, and barley) that leads to damage to the small intestinal lining. It can cause malabsorption, weight loss, and diarrhoea. But increasingly, research shows that many people – especially those with autoimmune conditions – don’t present with these “classic” gut symptoms.

While many people think of coeliac disease as a digestive condition, it’s actually a systemic autoimmune disease, and in many cases, the gut is not where the symptoms show up first (or at all). Especially in adults and those with other autoimmune conditions, the signs can be much more subtle or seemingly unrelated.

In fact, studies show that up to 60% of adults with coeliac disease are asymptomatic or experience only non-gastrointestinal symptoms. Instead of the classic diarrhoea, bloating, or weight loss, the body gives subtler but still significant signs that something isn’t right.

Instead, coeliac disease (or gluten-related disorders more broadly) may manifest as:

1. Iron deficiency anaemia

Take iron deficiency anaemia, for instance. The small intestine plays a crucial role in absorbing iron, folate, and B12. But when the intestinal lining becomes inflamed – whether or not you're experiencing gut symptoms – its ability to absorb nutrients can be severely impaired. 

Many people with undiagnosed coeliac disease experience persistently low ferritin or haemoglobin levels despite a nutrient-dense diet. For women in particular, this can be one of the first warning signs that something deeper is going on.

2. Neurological symptoms (brain fog, ataxia)

The nervous system, too, is a common target of gluten-related immune activation. Gluten ataxia, while rare, is a well-documented neurological manifestation of gluten sensitivity or coeliac disease. You may experience symptoms like brain fog, tingling, poor coordination, or memory issues. These symptoms are believed to result from anti-gliadin antibodies crossing the blood–brain barrier and triggering neuroinflammation, often in the absence of any digestive distress.

In my case, the response was almost immediate. Within a short time of eating gluten, I would experience sudden mood changes, including a deep sense of unease or irritability, followed by intense anxiety or even panic attacks. It took me years to make the connection, especially since these reactions weren’t accompanied by gut symptoms. But once I began removing gluten consistently, the emotional instability and neurological symptoms went away – an outcome I’ve since seen echoed in clients with similar autoimmune patterns.

3. Bone density loss (osteopaenia or osteoporosis)

Low bone density is another under-recognised manifestation. Because vitamin D, calcium, and magnesium absorption all depend on a healthy gut lining, those with undiagnosed coeliac disease are at greater risk of developing osteopaenia or even osteoporosis at a younger age. 

In some cases, coeliac disease is only diagnosed after an unexpected fracture or following a DEXA scan that reveals low bone mineral density. Chronic systemic inflammation further accelerates this bone loss.

4. Skin issues (dermatitis herpetiformis, alopecia)

Skin is another site where gluten sensitivity can leave a mark. Dermatitis herpetiformis is a classic example – an intensely itchy, blistering rash that typically appears on the elbows, knees, or scalp. But other dermatological manifestations, including eczema, psoriasis, and alopecia areata, are increasingly recognised in those with gluten-related immune dysregulation – conditions I’ve experienced personally and frequently see in clinic.

While these issues are often treated in isolation – usually with topical steroids or immunosuppressants – what’s often overlooked is the inflammatory trigger driving them from within. 

In both my own journey and my clinical practice, I’ve seen how powerful dietary changes can be in calming the immune system. For some, the transformation is subtle; for others, it’s dramatic. Either way, the skin often tells a deeper story, and gluten is a common thread.

5. Autoimmune thyroid disease (e.g. Hashimoto’s)

There’s also a well-established connection between coeliac disease and autoimmune thyroid disorders, particularly Hashimoto’s. Both conditions share genetic markers such as the HLA-DQ2 and DQ8 alleles. Gluten proteins may act as cross-reactive antigens, prompting the immune system to mistakenly attack thyroid tissue in those genetically predisposed. 

Clinically, removing gluten has been associated with reductions in thyroid antibody levels and, in some cases, a stabilisation of thyroid function.

6. Reproductive symptoms (infertility or irregular periods)

Finally, the impact of gluten-related autoimmunity on reproductive health is often missed. In both women and men, coeliac disease has been linked to delayed puberty, irregular periods, early menopause, and unexplained infertility. Inflammation, nutrient malabsorption, and hormonal disruption all play a role. 

Several studies have shown that removing gluten can help regulate menstrual cycles and support hormonal balance, especially in women with undiagnosed coeliac disease or gluten sensitivity. In practice, I’ve seen this play out in clients who had been trying to conceive for years without answers, only to find that eliminating gluten helped shift things in the right direction. For some, it was the missing piece that made everything else work better. It’s not a guaranteed fix, but it’s a meaningful option to explore when conventional tests don’t reveal the full picture.

All of this underscores the importance of considering gluten-related disorders when you have unexplained or multi-systemic symptoms, especially when autoimmunity is already part of the picture. The absence of gut symptoms does not rule out a gluten issue. In fact, in many cases, it’s the rest of the body that bears the brunt.

The autoimmune connection

Coeliac disease is itself an autoimmune condition, but it rarely appears alone.

People with coeliac disease have significantly higher risks of developing other autoimmune diseases, including:

• Hashimoto’s thyroiditis
• type 1 diabetes
• autoimmune hepatitis
• alopecia areata
• psoriasis
• Sjögren’s syndrome

And vice versa: if you already have one autoimmune condition, your risk of coeliac disease increases dramatically. One large study found that up to 8% of people with autoimmune thyroid disease also had coeliac disease, many of whom were unaware.

This co-occurrence is not a coincidence. Shared genetic predispositions (particularly HLA-DQ2 and DQ8), impaired gut barrier function ("leaky gut"), and dysregulated immune tolerance all contribute to this clustering.

False negative tests

A standard coeliac screen typically includes a test for tissue transglutaminase antibodies (tTG-IgA) and total serum IgA to rule out selective IgA deficiency, which can otherwise produce a false negative. Sometimes, deamidated gliadin peptide (DGP) antibodies are also measured, particularly in younger children or when tTG results are borderline.

However, these tests can miss cases. If gluten has already been reduced or eliminated from the diet, antibody levels may fall, even if intestinal damage is still present. 

In some people, antibodies normalise while tissue inflammation persists. Additionally, people with IgA deficiency – affecting about one in 500 – may not produce enough of the relevant antibodies to trigger a positive result.

There’s also the issue of non-coeliac gluten sensitivity. This condition doesn’t show up on conventional coeliac tests because it doesn't involve the same autoimmune response or intestinal damage. Yet symptoms can be just as disruptive, especially in those with a history of immune dysfunction.

In my case, I had already started cutting back on gluten by the time I was tested. I didn’t have classic gut symptoms, but I did have autoimmune markers, persistent fatigue, nutrient deficiencies, and a long history of alopecia areata. These are increasingly recognised in the literature as potential red flags for gluten-related immune activation – even in the absence of a formal coeliac diagnosis.

The link between coeliac disease and alopecia areata

The connection between coeliac disease and alopecia areata is one of the more overlooked but clinically important intersections in autoimmune health. While it’s often assumed that coeliac disease presents primarily with digestive symptoms, hair loss, particularly alopecia areata, can sometimes be the only visible sign. 

In fact, several case studies and small clinical trials have documented those with alopecia saw significant improvement, or even complete hair regrowth, after adopting a gluten-free diet. In many of these cases, coeliac disease was only diagnosed retrospectively, after the dietary shift led to a resolution of symptoms.

Interestingly, this connection appears particularly strong in children. Research has shown that children with alopecia areata tend to have a higher incidence of positive coeliac antibodies, even when they don’t display any gastrointestinal symptoms. A 2016 study published in the Dermatology Online Journal found that routine screening for coeliac disease in patients with alopecia areata uncovered a number of silent or subclinical cases that might otherwise have been missed. In these instances, hair loss was not just a cosmetic issue, it was a signpost pointing to an underlying immune imbalance driven, at least in part, by gluten exposure.

So, what’s the takeaway?

For anyone living with autoimmune disease – especially those with unexplained symptoms like hair loss, fatigue, or nutrient deficiencies – it’s worth considering the possibility of hidden gluten sensitivity or undiagnosed coeliac disease.

Even if standard tests come back negative, here’s what might be explored in clinic:

• genetic testing for HLA-DQ2/DQ8 to assess predisposition
• Zonulin or gut permeability markers
• nutrient testing (iron, B12, folate, zinc)
• a supervised gluten elimination trial, followed by a reintroduction phase to observe symptoms
• functional stool testing, as chronic inflammation may show up in the gut even without coeliac pathology

If symptoms improve significantly on a gluten-free diet – even in the absence of a formal diagnosis – it may be a sign that gluten is still playing a role in immune activation.

Autoimmunity rarely fits into tidy boxes. And neither does coeliac disease.

If you’ve ever been told “everything is normal” but your body is telling a different story, you’re not alone. A diagnosis isn’t always required to take action, and sometimes, removing a trigger like gluten is a key piece in calming the immune system, supporting gut healing, and even restoring hair growth.

When patterns point to gluten, even without a textbook diagnosis, I believe it’s worth listening.

References

• Wohl Y, Mashiah J, Drutin Y, Ben-Tov A. Coeliac disease risk doubles in patients with alopecia areata: a nationwide case-control study. Clin Exp Dermatol. 2025 Feb 24;50(3):648-650. doi: 10.1093/ced/llae489.
• Lebwohl B, Sanders DS, Green PHR. Coeliac disease. The Lancet. 2018;391(10115):70–81. doi:10.1016/S0140-6736(18)30038-2
• Waszczuk E, Waszczuk K, Zdanowski R, Więcek A. Coeliac disease and reproductive disorders: Meta-analysis and systematic review. Reproductive Biology and Endocrinology. 2021;19(1):130. doi:10.1186/s12958-021-00746-3
• Collin P, Reunala T, Pukkala E, Laippala P, Keyriläinen O, Pasternack A. Coeliac disease—associated disorders and survival. Gut. 1994;35(9):1215–1218. doi:10.1136/gut.35.9.1215
• Cohen AD, Dreiher J, Birkenfeld S. Coeliac disease and the skin. Dermatology Online Journal. 2016;22(5):13030/qt3mk9q72t. PMID: 27334242