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What exactly is autoimmune disease?

Written by Casey Wise | Wednesday, 20 July 2022


We understand the immune system to be an invaluable ally; protecting the body from any harmful pathogens it may encounter. But sometimes this powerful defensive armoury can turn against healthy cells and tissues, in what we refer to as ‘autoimmune disease.’

‘Autoimmune disease’ is a broad category of more than 80 disorders. Most of them are long-term illnesses and affect the body to varying degrees of severity. Prevalence is on the rise in Australia, with the latest health data estimating around 5% of Australians are affected by an autoimmune condition. This makes it a growing area of concern in natural medicine practice, especially given the complex nature of these conditions and the challenges of conventional treatment options.

So why exactly does the immune system turn on itself? Well, it doesn’t do so on purpose. Autoimmune disease occurs when the immune system loses the ability to distinguish between ‘foreign’ and ‘self’ antigens, and thinking that it’s under threat, mistakenly fires off antibodies to attack normal tissues. The target of the attack within the body varies with different types of autoimmune diseases. Some common examples include:

  • The joints: Rheumatoid arthritis
  • The thyroid: Hashimoto’s, Graves’
  • The nerves: Multiple sclerosis
  • The pancreas: Type I diabetes
  • The small intestine: Coeliac disease

But what are the underlying factors that cause this immune system dysregulation? Genetic predisposition is a key component, and, according to new research, so is sex. Autoimmune diseases affect women substantially more than men, which is solely due to them possessing two X chromosomes. The larger number of genes originating from the X chromosome increases the probability of a larger number of mutations occurring, thus putting women at greater risk for the development of autoimmune diseases.

However, genetics alone don’t guarantee disease. There are a host of environmental factors that can trigger the activation of an autoimmune state, including infection, stress, medications, intestinal permeability, poor diet, and lifestyle habits such as smoking. Hormonal changes during puberty and pregnancy for women (both at conception and during the postpartum period) can also be triggers for autoimmune disease.

The link between intestinal permeability and autoimmune disease is of particular interest within the complementary medicine field. The gut and the immune system have a symbiotic relationship and most of our immune cells (like T and B cells) reside within the gut. A healthy intestinal barrier contains mucosa with intact tight junctions, which allow for the safe passage of macromolecules through the gut. When the integrity of this mucosal lining is compromised (which can result from poor diet, toxin exposure, drugs, chemotherapy, etc.), the gut becomes permeable or “leaky”. This means that toxins, antigens, and bacteria have the potential to leak through the intestinal barrier and enter the bloodstream. Inflammation and immune system activation follow as these foreign particles are treated as threats to the body, and it is this persistent immune activation that can trigger autoimmune disease in genetically predisposed individuals.

While the complex interplay of genetics, environmental triggers, and intestinal permeability in autoimmune disease continues to be investigated, research findings to date reinforce the need for a holistic approach to the prevention and treatment of these conditions. With our focus on understanding each individual’s unique genetics and environment, natural medicine is perfectly positioned to assist patients in this space.


Angum, F., Khan, T., Kaler, J., Siddiqui, L., & Hussain, A. (2020). The prevalence of autoimmune disorders in women: A narrative review. Cureus, 12(5), e8094.

Hodson, R. (2021). Autoimmune disease. Nature, 595(45).

Mu, Q., Kirby, J., Reilly, C. M., & Luo, X. M. (2017). Leaky gut as a danger signal for autoimmune diseases. Frontiers in Immunology, 8, 598.

The Institute for Functional Medicine. (2022). Rise of autoimmune disease linked to intestinal permeability. Retrieved June 8, 2022, from

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Casey Wise

Casey is a practicing Clinical Nutritionist (BHSc Nutritional & Dietetic Medicine) and Endeavour College graduate based in Brisbane, Queensland. Her areas of expertise are autoimmune disease and gut health, and the interconnection between the two.

Casey's journey into nutrition began after being diagnosed with rheumatoid arthritis at just 17 years old and experiencing first-hand the transformative power of adopting a nutritious diet and healing the gut. This, combined with her education and clinical experience, has allowed Casey to develop a holistic and integrative approach to nutrition and cemented her passion for helping others to lead their healthiest, most fulfilling lives.

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