Skip to content

Autoimmune Diseases

Functional Medicine is a patient-centered, evidence-based approach to treating chronic diseases, including autoimmune conditions. In Functional Medicine we focus on the why? rather than just what? The what may be a diagnosis of diabetes. But why did you even get diabetes. Once we understand the cause(s), it’s easier to work on doing away with those cause(s).

Our focus is to identify and address the root causes of disease by understanding each patient’s unique genetic, biochemical, and lifestyle factors rather than the presenting symptoms.

Autoimmune diseases are caused by a malfunction of the immune system, that identifies the body’s own tissue as foreign and a potential threat.

In Functional Medicine we focus on the contributors for the development of the autoimmune reaction, which may include modulating the immune system, reducing inflammation, healing the gut, identifying and treating potential infections, managing stress, and balancing hormones.

Dietary Modifications

Unhealthy foods can promote inflammation, disrupt the gut microbiome, and even trigger autoimmune reactions. We recommend a diet high in nutrient-dense real whole foods and low in processed foods, sugars, and other potential inflammatory triggers. It’s important to evaluate which strategy is best for your personal circumstances and your preferences. Some commonly used food plans include:

  • Autoimmune Protocol (AIP) Diet: Potential food triggers such as grains, legumes, nightshades, dairy, eggs, coffee, alcohol, nuts and seeds, refined/processed sugars, oils, and food additives are eliminated from the diet. After a period of elimination and gut healing, foods are carefully and systematically reintroduced to identify potential triggers.
  • Paleo Diet: This diet focuses on lean meats, fruits, vegetables, and healthy fats, while eliminating grains, legumes, and dairy – which are considered to be more recent additions to the human diet and potential sources of inflammation.
  • Gluten-Free and/or Dairy-Free Diets: Some individuals with autoimmune conditions may be sensitive to gluten or dairy, and may benefit from removing these foods from their diet.


Supplements can support immune function, reduce inflammation, promote gut health, and address nutrient deficiencies. Supplements and dosage will be adjusted to your specific needs and may include:

  • Omega-3 fatty acids (EPA/DHA): Reduces inflammation which is commonly present in autoimmune diseases.
  • Vitamin D: It’s hardly possible to overestimate the importance of vitamin D and it’s no great surprise that it plays a crucial role in immune function. Significant vitamin D deficiency is often seen in autoimmune conditions Monitoring of blood levels is important. Often supplementation with magnesium and Vitamin K2 is needed.
  • Probiotics: Gut health is compromised in most cases of autoimmune diseases. Probiotic can help restore a healthy gut microbiome which can improve immune function and overall health. Doses may be significantly higher than usually recommended for probiotics.
  • Curcumin has potent anti-inflammatory and antioxidant effects.
  • Glutamine: This amino acid supports gut health and can aid in repairing the gut lining, which is often compromised in autoimmune conditions.

Stress Management of autoimmune disease

Stress can disrupt immune function and exacerbate many chronic diseases, including autoimmune conditions. Stress management techniques such as meditation, deep breathing, yoga, and mindfulness can help manage stress levels with a positive impact on the autoimmune response.

Exercise in autoimmune disease

Regular, moderate-intensity physical activity can support overall health, help manage stress, and may modulate immune function. It’s crucial to balance exercise with adequate rest to prevent overexertion, which can trigger an autoimmune flare.

Sleep and autoimmune disease

Adequate, high-quality sleep is critical for many aspects of health, including immune function and inflammation. Sleep disturbances can increase inflammation and potentially exacerbate autoimmune symptoms.

Identifying and Treating Infections

Identifying and treating chronic infections can help manage the autoimmune response. We may need comprehensive stool testing to assess the gut microbiome and identify any pathogenic bacteria, yeasts, or parasites that may be contributing to autoimmune disease activity. These tests may or may not be available in your state or country and may to be sent to specific labs for analysis.

Reducing Toxin Exposure

Toxins, both from the environment and from imbalances in the gut microbiome, can increase inflammation and disrupt immune function. This includes environmental toxins like heavy metals, chemicals in personal care products, and pesticides, as well as internal toxins like those produced by imbalanced gut bacteria.

Reducing toxic exposure is important. This may be achieved through using natural personal care and cleaning products, eating organic food as much as possible, and ensuring good indoor air quality.

Hormone Balance

Hormones have a significant effect on the immune system. Hormonal imbalances can disrupt immune function and trigger or exacerbate autoimmune symptoms. If relevant, then thyroid disorders, adrenal dysfunction, and sex hormone imbalances must be investigated and treated.

You are strongly advised to work with a healthcare provider experienced in Functional Medicine to develop and monitor a treatment plan.

This is especially true when it comes to supplement dosages, as these can vary widely depending on an individual’s specific needs and circumstances. Some supplements can interact with medications or have side effects, so they should always be used under the guidance of a Funnctional Medicine Doctor.


  • Cordain, L., Eaton, S. B., Sebastian, A., Mann, N., Lindeberg, S., Watkins, B. A., O’Keefe, J. H., & Brand-Miller, J. (2005). Origins and evolution of the Western diet: health implications for the 21st century. The American journal of clinical nutrition, 81(2), 341-354. Link
  • Ricker, M. A., & Haas, W. C. (2017). Anti-inflammatory diet in clinical practice: A review. Nutrition in Clinical Practice, 32(3), 318-325. Link
  • Calder, P. C. (2013). Omega-3 polyunsaturated fatty acids and inflammatory processes: nutrition or pharmacology? British journal of clinical pharmacology, 75(3), 645-662. Link
  • Hewison, M. (2012). An update on vitamin D and human immunity. Clinical endocrinology, 76(3), 315-325. Link
  • Maes, M., Leunis, J. C., Geffard, M., & Berk, M. (2014). Evidence for the existence of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) with and without abdominal discomfort (irritable bowel) syndrome. Neuro endocrinology letters, 35(6), 445-453. Link
  1. Daily, J. W., Yang, M., & Park, S. (2016). Efficacy of turmeric extracts and curcumin for alleviating the symptoms of joint arthritis: a systematic review and meta-analysis of randomized clinical trials. Journal of medicinal food, 19(8), 717-729. Link
  2. Kiecolt-Glaser, J. K., Bennett, J. M., Andridge, R., Peng, J., Shapiro, C. L., Malarkey, W. B., … & Layman, R. (2014). Yoga’s impact on inflammation, mood, and fatigue in breast cancer survivors: a randomized controlled trial. Journal of Clinical Oncology, 32(10), 1040. Link
  3. Dhabhar, F. S. (2014). Effects of stress on immune function: the good, the bad, and the beautiful. Immunologic research, 58(2-3), 193-210. Link
  4. Besedovsky, L., Lange, T., & Haack, M. (2019). The sleep-immune crosstalk in health and disease. Physiological reviews, 99(3), 1325-1380. Link
  5. Pärtty, A., & Kalliomäki, M. (2017). Infant colic is associated with low-grade systemic inflammation. J Pediatr Gastroenterol Nutr, 64(5), 691-695. Link
  6. Yu, X., & Zhang, J. (2018). Effects of indoor air pollutants on atopic dermatitis. International journal of environmental research and public health, 15(12), 2674. Link
  7. Tomljenovic, L., & Shaw, C.