The 7 Major Factors Causing AutoImmune Conditions

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autoimmune conditions

7 Major Factors Causing AutoImmunity

Autoimmune conditions, such as lupus, rheumatoid arthritis and MS, affect more than 250 million people worldwide. In the United States, they are the 3rd leading chronic diseases behind cardiovascular disease and cancer.

  • Have you, a friend, or family member been diagnosed with an autoimmune disease?
  • Do you have a family history of autoimmunity and want to learn how to prevent it?
  • Are you a healthcare provider who wants to better treat your autoimmune patients?
  • If that sounds like you, or you just want to learn more about treating and reversing these conditions, than this article is for you!

You will learn what I believe are the 7 major factors causing autoimmune conditions so you can understand why we have such an epidemic of chronic inflammation and autoimmunity.

Autoimmune Conditions Research:

Based on twin studies, we now know that 25% of autoimmune conditions are genetics, and the other 75% is environment (1).  I personally believe there are 7 main environmental factors causing  autoimmune conditions:

  1. Gluten Sensitivity
  2. GMO’s
  3. Gut Dysfunction
  4. Neurological Stress
  5. Toxins
  6. Stress and Adrenal Fatigue
  7. Infections

Every one of these is a piece of the pie–for some, one piece may be bigger–but all play a role to some degree.  As a clinician, I focus in on addressing all 7 of these areas to help people overcome their autoimmune conditions.  Here is the rationale and some research support for each area.

Gluten Sensitivity:

Gluten is the common protein found in wheat, barley, kamut, spelt & rye.  Gluten is a sticky, storage protein that challenges the digestive tract.   Gluten often binds to the small intestinal wall where it can cause digestive and immune system disorders.

Full-blown gluten allergies create destruction of the small intestinal villi (pockets that allow for nutrient absorption).  This condition is called Celiac disease but is not officially diagnosed until there is severe enough damage to the intestinal tissue to qualify for the diagnostic criteria of Celiac.

Non-Celiac Gluten Sensitivity (NCGS) is an epidemic that is a major contributing factor with inflammatory and autoimmune diseases.  For these individuals consuming gluten creates a chronic stress response that hyper inflames different regions of the body.

NCGS is highly associated with inflammatory disorders of all kinds (2).  It is also a contributing factor in many autoimmune diseases such as celiac disease, rheumatoid arthritis, type I diabetes, neurological disorders, Hashimoto’s thyroiditis, autoimmune cardiomyopathy, lymphoma, and dermatitis herpetiformis (skin disease) among others (3,4,5).   It is also linked as a contributing factor in asthma, allergies, & eczema (6,7).

Gluten, What is Gluten and Why is it so Bad?


In their position paper, the AAEM sites several animal studies that indicate extreme health risks associated with GM foods. Some of the health risks include infertility, immune dysfunction, allergic reactions, accelerated aging, insulin dysregulation, organ malfunction and digestive dysfunction (8).

The AAEM quoted in their paper, There is more than a casual association between GM foods and adverse health effects. There is causation, as defined by recognized scientific criteria. The strength of association and consistency between GM foods and disease is confirmed in several animal studies” (8)

Gut Dysfunction:

The gut plays a role in over 80% of the immune system and has a direct connection with the brain through the vagus nerve. Poor bacterial balance or dysbiosis is associated with every digestive tract disorder as well as auto-immune conditions and psychological and behavioral issues. The health of the body and mind are especially dependent upon the health of the human microbiome.

When the digestive system is damaged it leads to improper nutrient absorption and an increase in toxic substances in the body (9). This is one of the leading causes of chronic disease. For example, excessive yeast produces toxic substances that can pass through the blood-brain barrier and alter neurological functioning causing “brain fog,” behavior problems and learning difficulties.

Neurological Stress:

The nervous system and immune system are hardwired and work together to create optimal responses for the body to adapt and heal appropriately. Neural dysfunctions due to spinal misalignments are stressful to the body and cause abnormal changes that lead to a poorly coordinated immune response (10, 11, 12)

Birth trauma, bad posture over time and other traumas such as car accidents and falls affect and stress the spine.  In particular, these things can damage the vulnerable upper cervical spine which is extremely stressful to the body.  The ramifications of increased stress hormones in the body include overworked adrenal glands, lowered immunity, decreased digestive functions, fatigue, & blood pressure disturbances.

Subluxation is the term for misalignments of the spine that cause compression and irritation of nerve pathways affecting organ systems of the body. Subluxations are an example of physical nerve stress that affects neuronal control. According to researchers, neurological stress leads to altered measures of immune function & increased susceptibility to a variety of diseases (13, 14).

Seeing a chiropractor to help reduce subluxations and doing specific posture exercises that I go through in detail in this article along with possibly some other body therapies such as massage can be extremely helpful for your spine and nervous system.

autoimmune conditions

Toxins and Detoxification Ability:

The modern world is full of environmental toxins and these play a role in the development of autoimmune conditions.  It is estimated that there are over 80,000 toxic chemicals used regularly in the US.  There are over 500 chemicals stored in our body and the average individual has at least seven pesticides tested in their urine (15).  It is imperative to have a daily detoxification lifestyle to get these unwanted toxins out of our system.

The body has a built-in metabolic detoxification system to address this problem by converting fat soluble toxins into inactive water soluble metabolites.  This process is carried out by a series of enzymes that transform, conjugate (attach) and transport the toxins out of the body.

Many individuals have genetic polymorphisms that hamper their ability to detoxify.  Others have had their detoxification systems overwhelmed resulting in low glutathione and methylating elements.  Without these key factors, these individuals are unable to adapt and detoxify which allows oxidative stress and inflammation to be amplified.

autoimmune conditions

Stress and Hormones

Chronic, low-grade stress is a modern day epidemic that creates sluggish metabolism, chronic inflammation and abnormal immunity.  This stress depletes the body of critical nutrients and causes oxidation of various cellular elements.  Elevated stress hormone levels can create digestive problems and leaky gut syndrome, increased appetite, weight gain, thyroid disorders and accelerated brain degeneration (16).

These are common findings in the brains of those with anxiety disorders, depression and other psychological disorders.  Many auto-immune conditions have chronically elevated stress hormone production as a catalyst for this abnormal immune response (17).

Living in a state of fear is extremely destructive to human physiology.  Fear drives stress hormones which utilize all the key resources in the body and leave the system drained after a period of time.


Chronic parasitic infections are linked with intestinal permeability and leaky gut syndrome, irritable bowel syndrome, irregular bowel movements, malabsorption, gastritis, acid reflux, skin disorders, joint pain, seasonal and food allergies and decreased immunity (181920).

Other major infections include herpes, Lyme disease, human papilloma virus and cytomegalovirus, H pylori, small intestinal bacterial overgrowth (SIBO) and candida overgrowth.  There are many others, but all of these drain the immune system and cause abnormal reactions that can result in autoimmune conditions.  The main lab test I use to look at gut related infections is the GI MAP Stool Analysis here

autoimmune conditions

autoimmune conditions

The AutoImmune Elimination Program

I developed the AutoImmune Elimination program after years of research and clinical experience working with thousands of clients with autoimmune conditions and chronic inflammatory disorders.  This program goes over the key foundational strategies to address the major causes of chronic inflammation and leaky gut.

My hope and prayer is that this program provides you with the knowledge and tools to improve your life and heal naturally.  Be sure to check out the webinar I released where I did a specific training on the components of this program and how to put these things into action.

autoimmune conditions

Sources For This Article Include:

1. The Immunogenetic Architecture of Autoimmune Disease Link Here
2. Farnetti S, Zocco MA, Garcovich M, Gasbarrini A, Capristo E. Functional and metabolic disorders in celiac disease: new implications for nutritional treatment. J Med Food. 2014 Nov;17(11):1159-64. PMID: 25072743
3. Troncone R, Discepolo V. Celiac disease and autoimmunity. J Pediatr Gastroenterol Nutr. 2014 Jul;59 Suppl 1:S9-S11. PMID: 24979198
4. Cohn A, Sofia AM, Kupfer SS. Type 1 diabetes and celiac disease: clinical overlap and new insights into disease pathogenesis. Curr Diab Rep. 2014 Aug;14(8):517. PMID: 24952108
5. Valentino R, Savastano S, Maglio M, Paparo F, Ferrara F, Dorato M, Lombardi G, Troncone R. Markers of potential coeliac disease in patients with Hashimoto’s thyroiditis. Eur J Endocrinol. 2002 Apr;146(4):479-83. PMID: 11916614
6. Uvackova L, Skultety L, Bekesova S, McClain S, Hajduch M. The MS(E)-proteomic analysis of gliadins and glutenins in wheat grain identifies and quantifies proteins associated with celiac disease and baker’s asthma. J Proteomics. 2013 Nov 20;93:65-73. PMID: 23268118
7. Ohlsen BA. Acupuncture and a gluten-free diet relieve urticaria and eczema in a case of undiagnosed dermatitis herpetiformis and atypical or extraintestinal celiac disease: a case report. J Chiropr Med. 2011 Dec;10(4):294-300. PMID: 22654688
8. Vighi G, Marcucci F, Sensi L, Di Cara G, Frati F. Allergy and the gastrointestinal system. Clinical and Experimental Immunology. 2008;153:3-6.
9. Vighi G, Marcucci F, Sensi L, Di Cara G, Frati F. Allergy and the gastrointestinal system. Clinical and Experimental Immunology. 2008;153:3-6.
10. Sternberg EM, Chrousos GP, Wilder RL, Gold PW. The stress response and the regulation of inflammatory disease. Ann Intern Med. 1992 Nov 15;117(10):854-66. PMID: 1416562
11. Cizza G, Sternberg EM. The role of the hypothalamic-pituitary-adrenal axis in susceptibility to autoimmune/inflammatory disease. Immunomethods. 1994 Aug;5(1):73-8. PMID: 7842250
12. Wilder RL. Corticotropin releasing hormone and the hypothalamic-pituitary-adrenal axis in the regulation of inflammatory arthritis. Agents Actions Suppl. 1993;41:3-9. PMID: 8317340
13. Models of Vertebral Subluxation: A Review
14. Chiropractic boosts immunity Link Here
15. Methodology Link Here
16. Turner J, Kelly B. Emotional dimensions of chronic disease. Western Journal of Medicine. 2000;172(2):124-128.
17. Stojanovich L, Marisavljevich D. Stress as a trigger of autoimmune disease. Autoimmun Rev. 2008 Jan;7(3):209-13. PMID: 18190880
18. Intestinal Parasites, Bacterial Dysbiosis and Leaky Gut Link Here
19. Acid Reflux: A Red Flag Link Here
20. Do parasites cause autoimmune diseases? Link Here

c diff infection, C. Diff Infection: Risk Factors, Symptoms, and Support Strategies

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  1. Vaccination injects known and potent neurotoxins into the body. Because they are injected, they do not have a clear path out of the body, so they can accumulate. Aluminum (neurotoxicant), thimerisol (development toxicant), formaldehyde (carcinogen), phenoxyethanol (antifreeze), ammonium sulfate (neurotoxicant)…. the lists go on and on. We are literally poisoning the ones receiving the vaccinations. And there are NO independent double-blind studies even proving that vaccines are safe and effective. Where does poison fit into the health paradigm??? Please, ALWAYS read the vaccinations inserts (available online) BEFORE agreeing to vaccinations. The medical professionals often get paid or benefit by having patients vaccinated…. they rarely really know the true consequences of vaccines. You must learn the potential risks, and ingredients, for yourself.

      1. Realistically vaccines fall into all 7 categories:
        Gluten Sensitivity – vaccines contain yeast and the adjuvant stimulates an immune system response to the ingredients of the vaccine.
        GMO’s – vaccines have been shown to contain glyphosate – which is actually the bigger issue in the GMO debate
        Gut Dysfunction – Vaccines have been show to create this
        Neurological Stress – Vaccines have been show to create this
        Toxins – Vaccines include many toxins including aluminium, formaldehyde, polysorbate 80 etc.
        Stress and Adrenal Fatigue – Vaccines have been show to create this
        Infections – This is the premise of vaccines – get your body to think you are a little bit sick
        I am not saying Vaccines are the only reason for autoimmune disorders, but they definitely contribute to them in a significant way. Anyone interested read some of Yehuda Shoenfeld’s work on ASIA (Autoimmune Syndrome Induced by Adjuvants)

  2. Dear Dr Jockers
    I have been diagnosed with cidp and am undertaking IvIg therapy with great success .I was immensely stressed and ingested mould toxins . After being admitted to hospital with a crp of 579 mmol / l and neutropillia and leucophillia I had a thoracotomy for pleurisy , pneumonia and an empyema .
    How can I find the toxin and infective pathogen that caused my neuropathy and how can I determine how the stress contributed to my illness I am a ruminant nutritionist from Australia

    Thank you for your very informative and accurate information

    1. I am so sorry to hear about this Paul! I would recommend finding the best holistic practitioner in your area and get functional testing done! Praying for you!

  3. Hi Dr Jockers,

    I am 45 year old i am a female and have been undiagnosed now for 15 years with a Immune Disfunction i have been seen to by a group of Immunology Doctors at The Princess Alexander Hospital in Brisbane Australia,they are calling my Immune Disfunction Idiopathic CD3 Lymphopenia and Thrombocytopenia in the past also.I have suffered with Herpes since my early 20`s and was really hoping that you or might know of someone who could help me with this very frustrating health issue ???To look at me i look very healthy on the outside but not the case when my immune system fails my test results always show my platlets dropping and my DC4 count CD6 count progressivly always dropping,

    Would appreciate any advice you or other coullegues could advise,
    Regards Sandy Hamilton.

  4. Dear Dr. Jockers,
    A dear young friend of mine was diagnosis to have IgA in her early 20’s and she has been to several specialists who told her that it’s an autoimmune disease, which means it can’t be cured and that there is a chance of developing kidney failure later in life. She is a very beautiful lady in her early 30’s now and wants to dedicate herself as a missionary. I seldom hear doctors talk about IgA and wonder if this autoimmune disease is really very difficult to treat? Appreciate if you can give me advice on how she can improve or stabilize her condition.

    1. Hey Cecilia, I’m so sorry to hear about your friend! IgA Deficiency can sometimes be accompanied by autoimmunity. I would say start with the diet and remove anything that could be causing issues. That would be something like my Autoimmune Elimination Program:
      Then try implementing some of the strategies in these articles:

      She can also email to get some coaching on this!

  5. Your link to download The 3 Most Important Nutrients for Healing Autoimmunity isn’t working for me. I fill in my name and email address but there is no download link at the bottom of the page, as stated. I just get a Thank You with a big check mark page. HELP!

  6. All,
    If you are concerned about autoimmunity, you need to read the work of Anthony William, Medical Medium, and others, who bring light to the “autoimmune” misconception. Please be aware of the real problem behind immunodeficiency and inflammation. The body does NOT attack itself. It attacks pathogens and that’s what taxes the immune system. Gluten does not cause the body to attack itself, gluten feeds viruses and bacteria. You never mentioned Epstein-Barr virus family and that is the silent epidemic responsible for the explosion of so-called autoimmune disorders in the world.
    Seriously do yourself a huge favor and familiarize yourself with his work and that of those who have researched and vetted his theories, i. e. Kasia Kines CN and have come to scientific truths. We are a shrinking planet and the closer proximity we live in and share resources as well as travel all over, the more we share viruses and bacteria and the epidemic grows. Knowing the real truth behind our planetary illnesses will change your lives. Good luck to you!

  7. I’m so grateful I found Dr. Jockers website it’s helping me a lot I have struggled with poor health for decades I’m getting answers to all the ???? THANK YOU GOD BLESS YOU
    ordered a couple items already

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