Functional Medicine for Autoimmune Conditions:

A Root-Cause Approach to Healing

Autoimmune conditions are on the rise, affecting millions of people worldwide. These disorders occur when the immune system mistakenly attacks the body’s own cells, leading to chronic inflammation and a wide range of symptoms.

Unfortunately once you have one autoimmune condition, you are at risk to having more. This is because the condition is more accurately thought of as an immune dysfunction. Labelling diseases is helpful if you only want to take medications – as this is a top-down, one-sized-fits-all approach, but it rarely take the individual causes into consideration. For example, if you have inflammation, you may be prescribed an anti-inflammatory, however this approach is unlikely to address the source of the inflammation.

Biologics are a new branch of medications that can help to improve autoimmune disease symptoms, however they work by suppressing your immune system, which also increases your risk of infections and even cancers. 

Functional medicine takes a root-cause approach, which aims to restore balance to the body and support the immune system naturally. This is not simple or straight-forward, as the body is very complex and this is why functional medicine takes more time than conventional approaches. Although if we do our due diligence and we find and address your specific triggers and imbalances; the results can be outstanding. 

The Top 10 Autoimmune Conditions

Autoimmune diseases can affect nearly every organ and system in the body, as you can see from the disease manifestations below.

This is a list of 10 of the most common autoimmune conditions (as of 2025):

1. Rheumatoid Arthritis (RA) – A chronic inflammatory disorder affecting the joints.
2. Hashimoto’s Thyroiditis – A condition where the immune system attacks the thyroid, leading to hypothyroidism.
3. Graves’ Disease – An autoimmune disorder causing hyperthyroidism (an overactive thyroid).
4. Systemic Lupus Erythematosus (SLE) – A systemic condition that affects the skin, joints, and internal organs.
5. Multiple Sclerosis (MS) – A disease in which the immune system attacks the protective covering of nerves.
6. Type 1 Diabetes – An autoimmune condition in which the immune system destroys insulin-producing cells in the pancreas.
7. Coeliac Disease – An autoimmune response to gluten, leading to intestinal damage.
8. Psoriasis – A skin condition caused by an overactive immune response.
9. Psoriatic Arthritis – An inflammatory arthritis associated with psoriasis.
10. Inflammatory Bowel Disease (IBD) – Includes Crohn’s disease and ulcerative colitis, which cause chronic inflammation of the digestive tract.

However the list of autoimmune conditions continues to grow with more being diagnosed and labelled. I am definitely seeing more autoimmune conditions in the past 10 years and also see many client with undiagnosed autoimmunity, as they have varied disease processors – which once again highlights that autoimmunity is not about the disease, but instead about the person.

Here is a list of 10 more common autoimmune conditions.

• Ankylosing Spondylitis – A form of arthritis that primarily affects the spine.
• Sjögren’s Syndrome – An autoimmune disorder that affects moisture-producing glands, leading to dry eyes and mouth.
• Vitiligo – A condition where the immune system attacks pigment-producing cells, causing skin discoloration.
• Pernicious Anemia – An autoimmune attack on the cells that absorb vitamin B12, leading to deficiency.
• Addison’s Disease – A disorder where the immune system attacks the adrenal glands, reducing hormone production.
• Autoimmune Hepatitis – A condition in which the immune system attacks liver cells, leading to inflammation.
• Myasthenia Gravis – A condition that disrupts communication between nerves and muscles, causing weakness.
• Dermatomyositis – An inflammatory disease that causes muscle weakness and skin rash.
• Eosinophilic Oesophagitis (EoE) – A chronic immune system disease affecting the oesophagus.
• Autoimmune Urticaria – Chronic hives caused by an immune system malfunction.

Functional Medicine’s Approach to Autoimmune Conditions

Functional medicine differs from conventional treatments by focusing on identifying and addressing the root causes of immune dysfunction, instead of directly trying to suppress the disease process.

Regardless of the diagnosis, your practioner needs to be asking quality questions, such as:

• Why has the body reacted in this way?
• What are the triggers (known and other potential triggers that co-incided with the disease onset – e.g. hormone changes, stress, illness etc)?
• What are the mediators (things that continue to fuel the autoimmune dysfunction – e.g. diet, lifestyle factors, deficiencies etc)?
• What does the body need to re-establish immune balance?
• What needs to be eliminated or reduced to allow the immune system to calm down?

The answers to all of these things vary between people with the same autoimmune disease and this is why just targeting the disease is not the best approach. If we just “treat” the disease, the imbalance is allowed to continue which can result in additional autoimmune conditions over time.

Here are some key areas that are addressed in a functional medicine approach:

1. Gut Health and the Microbiome

The gut houses about 70% of the immune system, and imbalances in your gut microbiome (the rainforest of bacteria that is unique to you as your fingerprint) can contribute to autoimmunity. Functional medicine emphasises gut healing through:

• Eliminating trigger foods such as your specific immune-reactive foods and processed sugars.
• Improving your unique balance of intestinal bacteria through functional foods, fibres, prebiotics and probiotics.
• Healing your gut integrity and function to eliminate “leaky gut” or intestinal permeabililty and improve digestion and nutrient absorption and assimilation.

2. Identifying and Reducing Triggers

Autoimmune conditions are often triggered by infections, toxins, food sensitivities, and chronic stress. Functional medicine practitioners use testing, herbal medicine, dietary and lifestyle modifications to identify and eliminate these triggers.

3. Balancing the Immune System

Functional medicine aims to modulate and support immune function rather than simply suppressing the immune response. This is achieved through:

• Reducing triggers – Mental, emotional, physical and environmental.
• Improving your anti-inflammatory potential – through through diet and lifestyle adjustments
• Assessing and optimising the levels of key nutrients for immune balance – including vitamin D, omega-3 fatty acids, vitamin A and zinc.
• Stress management – through movement, support, mindfulness, meditation, and/or breathwork.
• Utilising Herbal medicines – to help restore balance specifically with evidence-based anti-inflammatory and immune mediating actions.

4. Addressing Nutrient Deficiencies

Common deficiencies (or in some cases excesses) in vitamin D, magnesium, selenium, iron, iodine and zinc can worsen or even trigger autoimmune symptoms. Functional medicine assesses pathology, functional testing and body signs and symptoms to assess nutrient requirements and addresses deficiencies using targeted nutrition and supplementation.

5. Detoxification and Reducing Toxin Exposure

Ongoing exposure to environmental toxins together with our individual toxin burden can contribute to immune dysfunction.

Aside from reducing exposures, functional medicine supports detox pathways if toxin load is thought or found to be a contributing issue. Supplementation may be suggested to support any body system imbalances.

Some suggestions may include:

• Clean, hydrating, (ideally) organic food choices.
• Regular sweating through exercise or sauna therapy.
• Liver-supporting & bowel-supporting foods like phytonutrients (health promoting plant chemicals), fibre, cruciferous vegetables (broccoli, kale, Brussel sprouts etc) and herbal medicines including dandelion root and globe artichoke.
• Nutraceutical supplementation may include n-acetyl cysteine, glutathione, selenium, vitamin D or zinc.

A personal, structured wellness plan is essential

Autoimmune conditions require a personalised and holistic approach. Our functional medicine approach empowers individuals to take control of their health by addressing root causes and making sustainable lifestyle changes. While there is no one-size-fits-all solution, many people experience significant improvement by focusing on gut health, reducing inflammation, and supporting immune balance.

Get in touch to find out how a functional medicine approach can help to restore immune balance and improve your health.