Autoimmune Disease: The 5 Main Causes of Autoimmunity & How to Reverse It

What is autoimmunity (autoimmune disease)?

In response to an unknown trigger, the immune system may begin producing antibodies that instead of fighting infections, attack the body’s own tissues. Examples of autoimmune diseases include: Hashimotos thyroiditis, Rheumatoid Arthritis, Multiple Sclerosis, Lupus, among others.

Standard treatment of autoimmunity is to shut down the immune system, which comes with a host of possible long-term side effects such as increased risk of cancer and risk of increased chronic and acute infections. I see the goal of treatment is to be able to significantly reduce or get off of the DMARDs (Disease Modifying Anti-Rheumatic Drugs), Steroids (prednisone), chemotherapy medications AND to see autoimmune markers go into remission. You can have 10 people with the same autoimmune disease, and need to treat each one a little differently. Currently 80 million people in the US have a type of autoimmune disease.

Examples of recovery of autoimmunity…


  1. Dr. Terri Wahl, MD – had chronic multiple sclerosis, and was failing drug therapy, body was failing, could not get out of the wheelchair. She went into every category listed here, and she reversed her autoimmunity. She has high levels of mercury and lead, many food allergies, gut infections and chemical exposure.
  2. Joe Cross, from Fat, Sick and Nearly Dead. He did a 60-day juice cleanse of mostly vegetables and green apples – lost 67 lbs and reversed his rare autoimmune disease and came off all of his medications.
  3. Patient with ALS working with functional medicine physician who underwent intensive regenerative, holistic treatment (hyperbaric oxygen chamber, ozone therapy, stem cell therapy) along with all of the recommendations below, was able to reverse his ALS to be able to walk and stand again.

If you have autoimmune disease, use this guide to start your journey towards a healthy recovery!

The Top 5 Causes/Contributors to Autoimmunity and Inflammation

  • Toxins (Metals, Chemicals, Mycotoxins, Pesticides)
  • Food allergens (IgA/IgG/IgE) and Environmental triggers
  • Microbiome (disrupted gut)
  • SAD (Standard America Diet) Diet
  • Stress – physical or mental stress


Where to begin?

Part of this recommendation can be started on your own, but I highly recommend looping us in or your local naturopathic or functional medicine doctor. Dr. Mark Hyman, MD recommends that his patients begin with his 10-day Detox Diet, which I fully support. He mentions that people can begin to see changes in their bodies even within this 10-day challenge.


To begin working on clearing up your functioning pathways, I would begin here:


  1. Identify and Eliminate Top Inflammatory Foods and Personal Food Allergens
    1. Eliminate top inflammatory foods
      1. Gluten
      2. Dairy
      3. Corn
      4. Eggs
      5. Soy
      6. Nuts
      7. Sugar
    2. Identify and eliminate your top food allergens – I would recommend testing these. We like US Biotek Food Allergy Panel IgA/IgG x 96 foods.
  2. Correct dysbiosis and heal the microbiome
    1. What does the gut and the microbiome help us do?
    2. Makes most (think 80%) of our brain neurotransmitters such as dopamine, serotonin, epinephrine and norepinephrine
    3. Helps our metabolism and to absorb our vitamins and nutrients
    4. Heals our gut lining, maintaining the integrity of the our gut barrier
    5. Modulates (regulates) our immune system (thought that 70-80% of our immune cells are in the gut)
    6. Protects us against pathogens (microorganism that is harmful)
  3. Treat the hidden infections (Lyme, Other tick infection, CMV, EBV, SIBO)  Remember, it is possible to have more than one chronic infection, and to not remember ‘catching’ that infection. It is really common for the people I see to swear that they never have caught mono, yet the reactivated antibodies for mono that are positive in their system tell a much different story. This tells you how important being tested is, as opposed to relying on your interpretation of your own symptoms and history.
  4. Identify toxin levels Identify areas of exposure in your past and in your current environment. For example, if you remember growing up in an old house, there might be past lead exposure. Or if you remember being in a moldy environment, you could still be carrying mold (myco) toxins in your system. Another example is working in an environment where you are having current exposure. I see this with people especially who are working in manufacturing, which tends to be higher in metal (cadmium and lead) and chemical (solvents) exposure. Look for exposure to heavy metals, chemical (herbicides, pesticides and plastics) and complete the testing to identify levels.
  5. Identify stressors Most of us know when we are experiencing stress and sometimes it can be difficulty to step back and bring in tools to help you manage. I highly recommend talking with someone (counselor/your doctor) if you are experiencing stress that feels unmanageable, as there are many tools we can provide to help make things feel more manageable. Some resources that I love are for helping to find peaceful times and moments are:
    1. Calm App – meditations and calming stories to help relieve stress
    2. Insight Timer – 30,000+ meditations, tunes, visualizations and courses for feeling calm and well
    3. Infrared Sauna – 15-30 minutes at anywhere from 125 to 165 degrees – incredibly relaxing and calming, with the bonus of detoxing as well


An Example Treatment Plan for Reversing Autoimmunity


  1. Correct your Vitamin D3 levels (helps to modulate the immune system); I want to see levels between 70-80 in the blood.
  2. Increase anti-inflammatory oils – Fish oil – 2-3,000mg per day with food.
  3. Increase anti-inflammatory herbs – Turmeric, Quercetin, Bromelain, Frankincense (away from food
  4. Begin identifying and eliminating inflammatory foods
  5. Incorporate a stress-relieving regimen into your daily routine
  6. Work with your Naturopathic or Functional medicine physician to begin diving into deeper, more extensive testing:
    1. Challenged Urine Heavy Metal Panel (collect for at least 8 hours)
    2. Urine Chemical Testing
    3. Urine Mycotoxin (mold) Testing
    4. Comprehensive Stool Panel looking at an extensive stool culture of healthy and pathogenic bacteria, fungus and parasites (see Genova’s GI Effects Comprehensive Stool panel as an example)
    5. Extensive bloodwork which looks for balance of thyroid, adrenals, vitamins, minerals, presence of chronic viruses, immune markers, inflammatory markers


If you would like guidance in any of these areas, we would love to see you! We love creating personalized health plans for patients, and would love to do so for you! Please reach out if you have questions!

In love, health and light,

Dr. Angila Jaeggli, ND

Phone: (425) 835-0359

Sage Integrative Medicine Clinic, PLLC

110 James Street, Suite 103

Edmonds, WA 98020

Instagram: drangilajaeggli

Youtube: Sage Health TV

Posted in

Dr. Angila Jaeggli