Guide
Autoimmune conditions: what a root-cause assessment adds, and what it does not
A root-cause assessment for autoimmune disease works alongside rheumatology, never instead of it. It looks for treatable contributors - deficiency, thyroid disease, coeliac disease, sleep, smoking - that specialist clinics rarely have time to cover. The aim is better control, not cure.
Who this guide is for
If you have an autoimmune diagnosis, your bloods are stable, your consultant is satisfied, and you still feel unwell much of the time, this is written for you. It is also for people with a strong family history who want to know what, if anything, can be done before something declares itself.
I am a hospital doctor who also runs a private functional medicine practice in Twickenham and Richmond, and online. I see a good deal of autoimmune disease: thyroid, rheumatoid, lupus, inflammatory bowel disease, coeliac disease, and the people who have several at once.
I have a commercial interest in you deciding to see someone privately. Read the next two sections before the rest.
The thing that matters most
I say this first because autoimmune disease attracts more 'root cause' marketing than almost anything else, and some of it is explicitly anti-medication. If a clinic's pitch involves coming off your treatment, leave.
What rheumatology does well
Modern specialist care for autoimmune disease is genuinely good, and it is free. Treat-to-target management of rheumatoid arthritis, guided by NICE NG100, has changed the outlook for that condition considerably in twenty years. The same is true across much of the field.
What specialist clinics do: confirm the diagnosis, suppress the immune activity, monitor for damage and for drug side effects, and escalate when control is lost. What they largely do not do, because appointments are short and the remit is the disease rather than the person, is look at everything sitting around the condition.
So the honest framing is not 'conventional versus root cause'. It is that one system manages the disease and there is a gap beside it.
How a root-cause assessment actually differs
This is the question people ask most often, so here is a direct answer rather than a philosophy.
| Specialist rheumatology or gastroenterology | Functional medicine assessment | |
|---|---|---|
| Main question | Is the disease active, and is the treatment controlling it? | What else is contributing to how you feel, and is any of it treatable? |
| Appointment length | Typically 10 to 20 minutes at follow-up | Two hours at first assessment |
| What is measured | Disease activity scores, inflammatory markers, drug monitoring, imaging | The above, plus deficiency, thyroid, coeliac, sleep, and the things that track with flares |
| What it can do | Diagnose, prescribe immunosuppression and biologics, monitor for damage | Address contributors, support diet and sleep, and refer back when the disease itself needs attention |
| What it cannot do | Much about fatigue, sleep, diet or the day-to-day when the bloods look fine | Replace immunosuppression. Nothing here controls active disease |
| Cost | Free on the NHS | Self-funded. Almost no insurance covers it |
Put simply: they treat the disease, and I look at the person around it. Both are needed, and if you can only have one, have the first.
What is worth investigating
These are the things I look for, chosen because they are common in autoimmune disease, they are measurable, and finding them changes what happens next.
- Other autoimmune conditions. They cluster. Autoimmune thyroid disease, coeliac disease and pernicious anaemia travel together and with others, and a second condition is often missed because the first one explains the symptoms plausibly enough. Coeliac serology and thyroid antibodies are cheap and frequently revealing.
- Vitamin D. Low levels are common in autoimmune disease. The VITAL randomised trial found that vitamin D supplementation over five years reduced the incidence of new autoimmune disease by around 22%, which is the best evidence there is that this is more than a marker.
- Iron, B12 and folate. Fatigue in autoimmune disease is often assumed to be the disease. Sometimes it is anaemia of chronic disease, and sometimes it is straightforward iron deficiency that nobody checked.
- Thyroid function properly interpreted. Including in people already on replacement, where the dose is often set and forgotten.
- Sleep, including sleep apnoea. Poor sleep worsens pain, fatigue and inflammatory markers. It is treatable and it is routinely missed.
- Smoking. The strongest modifiable risk factor for rheumatoid arthritis, and it reduces how well treatment works. I will raise it, once, without lecturing.
- Medication review. Including whether anything you are taking is contributing to the symptoms attributed to the disease.
Tests I will tell you not to buy
The same discipline as everywhere else on this site: a test is worth having if an abnormal result would change what I do.
IgG food antibody panels
Sold heavily to people with autoimmune disease, on the theory that identifying reactive foods will calm the immune system. IgG antibodies to food are a normal finding and largely reflect what you eat. They do not identify a driver of autoimmunity, and the main consequence of acting on them is an unnecessarily narrow diet in people who often already struggle to eat well.
Direct-to-consumer autoimmune screening panels
Broad antibody panels ordered without a clinical question produce false positives. A low-titre antinuclear antibody is found in a meaningful proportion of healthy people, particularly women, and without symptoms it usually means nothing. What it reliably produces is anxiety and a sequence of further tests.
Antibody testing is useful when it answers a specific question raised by a history and an examination. It is not a screening tool.
Leaky gut and zonulin testing
Intestinal permeability is a genuine research interest in autoimmunity, and the commercial serum zonulin assay is not a reliable way to measure it. A result either way would not change my plan.
Hair mineral analysis, applied kinesiology, bioresonance
No evidence base for autoimmune disease, or for much else.
Diet: what the evidence actually supports
Diet is where most of the claims are made and where the evidence is thinnest, so it is worth separating what is reasonable from what is oversold.
A Mediterranean-style diet has the most support. Trial evidence in rheumatoid arthritis is modest but real, and the wider cardiovascular benefit matters independently, because autoimmune disease raises cardiovascular risk.
The autoimmune protocol (AIP) is a strict elimination diet promoted widely for these conditions. The published studies are small, short and uncontrolled - a handful of participants, no comparison group - and they report symptom improvement without being able to show that the diet caused it. I will support someone through a time-limited trial if they want one, with reintroduction planned from the start. I will not tell you it is evidence-based, because it is not.
Gluten is non-negotiable in confirmed coeliac disease and unproven in other autoimmune conditions. If you want to test whether it matters for you, get coeliac serology done first, while you are still eating it.
What I am wary of is any diet presented as permanent, restrictive and curative. The people I see with autoimmune disease are frequently underweight, tired and eating from a shrinking list of foods, and the diet is making that worse rather than better.
A realistic aim
Autoimmune disease is not cured by this work. It can often be better controlled, and people frequently feel considerably better without their disease activity score changing at all, because a good part of how they felt was deficiency, poor sleep, an untreated second condition or a medication side effect.
That is a worthwhile outcome and it is the one I aim at. Anyone promising remission or cure from diet and supplements is making a claim that the evidence does not support and that UK advertising rules do not permit.
What it costs, and the trade-offs
My fees are set out in full on the fees page. Testing is separate and usually the larger cost, and you should have a written estimate before anything is ordered.
| In favour | Against |
|---|---|
| Two hours at first assessment, enough to cover what short follow-ups cannot | You pay for it, and there is no NHS or insurance route |
| Contributors found and treated that nobody had looked for | None of it controls the disease itself |
| One person who sees the whole picture across several conditions | A rheumatologist knows far more about your disease than I do |
| I write to your consultant and GP, and refer back when the disease needs attention | Adds a third party to coordinate with |
| Time to talk about diet, sleep and fatigue properly | The evidence for dietary intervention in autoimmunity is weaker than the marketing suggests |
If your disease is poorly controlled, the most valuable appointment available to you is with your specialist, not with me.
About the writer
I am Dr Andrew Greenland, GMC 4419909. I qualified in London in 1997, I am a Fellow of the Royal College of Emergency Medicine, and I still work at consultant level in an NHS hospital in west London alongside my private practice. I am a certified functional medicine practitioner.
I see patients in Twickenham and Richmond in Greater London, and online across the UK. I write to patients' GPs and consultants with their consent, and I see every patient myself.
Common questions
How does a root-cause approach differ from conventional treatment for autoimmune issues?
Conventional specialist care asks whether the disease is active and whether treatment is controlling it, and it is good at both. A root-cause assessment asks what else is contributing to how you feel and whether any of it is treatable - deficiency, an undiagnosed second autoimmune condition, thyroid disease, sleep apnoea, smoking, a medication side effect. It works alongside specialist care and it does not replace immunosuppression.
Will I have to stop my medication?
No, and you should be wary of anyone who suggests it. Disease-modifying drugs and biologics prevent joint destruction, organ damage and sight loss. If your medication is causing problems, that is a conversation with the prescriber, and I will write to them setting out what I have found.
Can diet cure autoimmune disease?
No. A Mediterranean-style diet has modest trial support in rheumatoid arthritis and a clear cardiovascular benefit that matters here. The autoimmune protocol has only small uncontrolled studies behind it. Diet can help how you feel and it is worth attention, but nothing in the evidence supports cure, and the restrictive diets often do harm in people who are already struggling to eat enough.
I have a family history but no diagnosis. Is there anything worth doing?
Possibly. Not smoking is the clearest single thing for rheumatoid arthritis. Vitamin D sufficiency has randomised evidence behind it from the VITAL trial. Beyond that I would want to know what runs in your family, because it changes what is worth checking. I would not run a broad antibody screen on someone without symptoms - it generates false positives and anxiety more reliably than it generates answers.
Do you handle complex cases with several conditions at once?
That is most of what I see in this area, and it is where a long appointment earns its keep, because the conditions interact and the specialists for each tend to see only their own. I will always want to know who else is involved in your care, and I write to them.
Sources
- NICE NG100. Rheumatoid arthritis in adults: management.
- Hahn J et al. Vitamin D and marine omega 3 fatty acid supplementation and incident autoimmune disease: VITAL randomised controlled trial. BMJ 2022.
- Sköldstam L et al. An experimental study of a Mediterranean diet intervention for patients with rheumatoid arthritis. Ann Rheum Dis 2003.
- Konijeti GG et al. Efficacy of the autoimmune protocol diet for inflammatory bowel disease. Inflamm Bowel Dis 2017.
- Sugiyama D et al. Impact of smoking as a risk factor for developing rheumatoid arthritis: meta-analysis. Ann Rheum Dis 2010.
Written and reviewed by Dr Andrew Greenland, MBBS, MRCSEd, FRCEM, FMCP-M, a practising hospital doctor and certified functional medicine practitioner. Registered with the General Medical Council, number 4419909(verify). This guide is general information and not a substitute for individual medical advice.
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