Autoimmunity: beyond the diagnosis
Receiving a diagnosis of an autoimmune disease can be frightening and it's natural to ask: why did this happen to me? Is there anything I can do beyond taking medication? Conventional medicine is excellent at diagnosing autoimmune diseases and controlling inflammation, often with life-changing medication. My work complements it. Rather than asking only what disease does this person have?, I ask a different question: why has this person's immune system become dysregulated?
What is an autoimmune disease?
Your immune system is designed to protect you from harmful invaders like bacteria and viruses. Medicine believes that in autoimmune disease, that defense system mistakenly attacks your own tissues. The target depends on the condition. In Hashimoto's, it's the thyroid. In rheumatoid arthritis, the joints. In multiple sclerosis, the nervous system. In psoriasis, the skin. In Addison’s disease, it’s the adrenal cortex, etc.
My theory is that because the immune system is incredibly smart, it doesn't simply wake up one day and randomly decide to attack healthy tissue. Rather than assuming the immune system "gets confused", I think it's more useful to ask what changed in the target tissue? Has the tissue been altered by chronic inflammation, oxidative stress, persistent infection or environmental exposures? We don't yet know the full answer for every autoimmune disease, but these are exactly the questions modern immunology continues to explore.
Although autoimmune diseases present differently, they share the same underlying drivers:
The Autoimmune Triangle
One of the best-known concepts in functional medicine is the Autoimmune Triangle, based largely on the work of Dr Alessio Fasano. It suggests that three factors generally come together before autoimmune disease develops:
1. Genetic susceptibility
Genes can increase your risk, but they do not determine your future. There isn't one "autoimmune gene." Instead, many genes influence how your immune system functions, how well your gut barrier works and how your body responds to inflammation and stress.
2. A trigger
Something usually needs to activate that genetic susceptibility. Often it's not one event, but several occurring together over time. Triggers vary from person to person and may include:
infections
chronic stress
poor sleep
overexercising
hormonal changes
nutrient deficiencies
environmental toxins incl. mould and heavy metals
certain medications
smoking
prolonged calorie restriction
blood sugar instability
3. ‘The leaky gut’
Research increasingly suggests that disruption of the intestinal barrier, commonly referred to as "leaky gut", plays an important role in many autoimmune diseases. While the evidence is strongest for some conditions, such as coeliac disease, maintaining a healthy gut barrier has become an important focus of functional medicine because the gut is closely connected to immune regulation. Read here why I often start by taking clients off gluten and dairy.
Looking beyond the diagnosis
The diagnosis itself is only one piece of the puzzle. When I work with someone who has an autoimmune condition, I'm interested in understanding what is driving their immune system to remain overactive.
Some of the questions I ask include:
What stage of autoimmunity is present (silent autoimmunity? positive antibodies without symptoms?
reactive autoimmunity? established autoimmune disease?)
Are there other autoimmune processes developing?
Is chronic stress keeping the immune system activated?
How well is the person sleeping?
Is blood sugar stable throughout the day?
Are there signs of digestive dysfunction or gut barrier impairment?
Could chronic infections be contributing?
Are there nutrient deficiencies?
Are environmental toxins or certain medications playing a role?
Are there lifestyle habits that continue to fuel inflammation?
Every answer provides another piece of the puzzle.
There is no "one cause" and no one solution
One of the biggest misconceptions about autoimmune disease is that there is a single cause. In reality, it is usually the result of multiple factors interacting over many years.
Two people with Hashimoto's thyroiditis may have completely different underlying drivers. One may have experienced years of chronic stress and poor sleep. Another may have developed symptoms after a viral infection. Someone else may have significant digestive dysfunction or nutritional deficiencies. This is why personalised care matters.
Which autoimmune protocol is best?
There is no shortage of protocols claiming to be the answer. The Autoimmune Protocol (AIP), the Wahls Protocol, carnivore, ketogenic diets, plant-based and even vegan approaches all have passionate advocates and thousands of success stories. Yet, people also fail on every one of them. Why? Because we are all different.
We digest food differently. We have different microbiomes, genetics, food tolerances, nutrient needs and lifestyles. A diet that transforms one person's health may make another feel worse. What successful approaches usually have in common isn't the name of the diet but the fundamentals; the so-called ‘non-negotiables’:
People who improve often prioritise:
whole, minimally processed foods
regular, balanced meals that support stable blood sugar
restorative sleep
stress management
sleep
correcting nutrient deficiencies
supporting gut health
movement that suits their body
You cannot supplement yourself out of poor lifestyle habits. These foundations often matter far more than focusing on the nitty-gritty details.
As a practitioner, I don't believe in forcing every client into the same protocol. I treat the person, not the diagnosis. A protocol can be a useful starting point, but true long-term success comes from understanding what your body needs rather than following a one-size-fits-all plan.
Can autoimmune disease go into remission?
Depending on the condition, remission is possible. For some people, symptoms become significantly quieter. Others experience long periods of stability with little disease activity. Functional medicine does not promise to cure autoimmune disease. Instead, the goal is to create the best possible environment for your immune system to function more appropriately by addressing the factors that are keeping it activated. This may include improving nutrition, supporting gut health, correcting deficiencies, managing stress, treating chronic infections where appropriate and optimising sleep.
The bottom line
Autoimmune disease is rarely caused by a single food, one infection or one stressful event. More often, it develops when genetic susceptibility, environmental triggers and immune dysregulation converge over time. The encouraging news is that while we cannot change our genes, we can influence many of the factors that affect how those genes are expressed. The diagnosis is only the beginning. By understanding the unique drivers behind your condition, it is often possible to reduce unnecessary immune activation, improve symptoms and support better long-term health.