Eric Bakker N.D.April 1, 2022

There are many different theories regarding the cause of auto-immune disease, the illness of "no known cause". Research is finding a connection with the gut, digestive health and the stress people face. as plausible causes.


What Causes Autoimmune Disease?

The infection and disease theory

On a very basic level, an autoimmune disease develops when the body’s natural defences, the immune system, targets healthy tissue. Scientists and researchers have several opinions as to why may occurs. When the immune system detects a virus or infection, it kicks into high gear and fights it. This reaction can sometimes involve healthy cells and tissues, resulting in autoimmune illness.

Rheumatoid arthritis, an autoimmune disease that attacks the smaller joints, is thought to be caused by this, according to research. People with strep throat are also more likely to develop psoriasis, an inflammatory disease that involves thick, scaly skin patches. Other types of autoimmune disease may result from the body’s attempt to fight cancer cells specifically. Scleroderma is a disease that causes skin and connective tissue thickening. The theory is that when the immune system eliminates the cancer, there is a residual inflammatory response from the struggle.

Articles of interest:

The Damage Theory

Injury, according to scientists, may play a role in some autoimmune diseases, such as psoriatic arthritis, which affects the joints of some patients with psoriasis. An autoimmune reaction occurs following damage to tendons, which connect muscle to bone, in sections of the body subjected to extreme stress, according to research. A runner’s heel, for example, is a region where the muscle pulls on the bone to create movement.

Repeated stress can expose the body’s tissue that shouldn’t be in contact with blood cells, It’s like a tiny wound when that tissue is exposed.  Blood cells try to repair it, but a faulty immune response causes joint and tendon inflammation. While there is some evidence to back them up, scientists have yet to show that they are the cause of autoimmune disease.

Genetic Theory

It’s clear that genes have something to do with autoimmune diseases, but scientists still don’t truly grasp how. For example, your risk of developing lupus or multiple sclerosis (MS) goes up if someone in your family has these diseases. Several people in some families have different autoimmune diseases. But autoimmune disease can’t be caused by genes alone. There are also many people who develop autoimmune diseases without having any relatives who did.

We know that genes are important, but they’re not everything. Research has found that if someone in your family has lupus or MS, it doesn’t necessarily mean you will get it.

It’s possible that autoimmune diseases happen because of how well the immune system deals with stress. Stress and autoimmunity is a well researched area, and the connection does exist. At what point does the stress on your body go beyond what your immune system can handle? If we knew this, we might be able to stop autoimmune diseases from happening. I’ll be explaining the link between stress and autoimmune disease very shortly.

The Hygiene Hypothesis

There has been a lot of attention paid recently to the  so-called hygiene hypothesis and its link possibly to autoimmune disease. The hygiene hypothesis basically is the theory that by living is a “sterile” environment and not being exposed to germs, especially during early childhood, the immune system is not properly “trained” and, lacking any real invaders to attack, and may begin to develop improper immune responses to non-pathogenic substances and may the immune system under these conditions may even attack the body’s own cells.
I’m one of those of the belief that it is important for a child to be exposed to germs in their environment; as this is how immunity develops into a strong and resilient inner force, capable of defending the body against a wide range of pathogens, as well as being more than able to handle recognising self from non-self.
We worry needlessly about germs on the one hand, whilst we pollute our minds and bodies with the effects of stress and environmental toxins (cell phones, chemicals, food additives, etc) on the other which we perceive as safe. Is it any wonder our immune systems are being adversely affected?

Are you worried about auto-immune issues? Then regardless if you have an auto-immune disease or not, improve your immunity in general by ensuring that it remains vibrant and strong naturally by consuming antioxidant vitamins A, C & E, herbs like echinacea & goldenseal, consuming a healthy diet, undergoing a regular detox as well as being aware of how stress affects your immune system.

You also improve your immunity by decreasing potentially high-risk behaviours like junk or processed foods, inactivity and/or obesity, the consumption of regular alcohol and tobacco, by not washing your hands and by being exposed to toxins and chemicals and pharmaceutical drugs. If your resistance and inter-personal transmission is slow (through good hygiene) your health increases because your susceptibility has been decreased.

If, on the other hand, your resistance is very weak (poor health) and poor immunity is favoured by poor hygiene, poisons, stress, etc, then the opportunity is created not only for all sorts of fast-growing and highly virulent strains of bugs (bacteria, viruses, yeasts) to dominate, the opportunity is also there for your immune system to go “off the rails”. It can literally have a mind of its own like a teenager, it does as it pleases and it may prove quite unpredictable indeed.

Environmental Toxicity And Autoimmune Disease

According to Dr. Hess, Professor of Medicine (University of Cincinnati College of Medicine USA): “Anything we eat, drink, breathe or absorb into our bodies can be environmental agents that trigger autoimmune diseases.”
Researchers from the University of California reported a long list of xenobiotic (foreign) substances that were examined. Many of these substances were found to trigger an autoimmune response. The list of known substances that trigger antibodies to attack their own tissues includes: mercury, vinyl chloride, silica, UV radiation and ozone, and there are many more to add to this list.
According to Dr. Walter Crinnion, A US expert in Environmental Medicine (linking disease with poisons, chemicals and heavy metals in our environment) the development of autoimmunity has long been linked with chemical exposure.
The notion of chemically-induced autoimmune states is not new, since many chemicals are known to induce the onset of systemic lupus erythematosis (SLE).
Pharmaceutical drugs that have been definitively associated with “drug-related” lupus include: chlorpromazine, hydralazine, methyldopa, and minocycline. Since the 1940’s, at least 70 pharmaceutical drugs and other agents have been linked with autoimmune diseases.
Some chemicals, including formaldehyde and other volatile organic compounds (VOCs), are thought to induce tissue-specific autoimmune reactions by acting as “haptens”.
These extremely tiny molecules bind to various tissues in the body, making a new toxin our immune system reacts too. The immune system then produces antibodies to this new combination, which can attack the “parent” tissue with or without the chemicals even being present.
Many people who have been exposed to certain chemicals often present with elevated antibodies to certain of their body tissues, including anti-myelin (nervous system), anti-parietal (stomach), anti-brush border and anti-smooth muscle (bowel) antibodies. And the more toxins you take in, the more likely your immune system will behave like that teenager.

Toxins Affect You 3 Ways

A study of 298 patients with exposure to industrial chemicals showed that environmental chemicals can affect your body’s immune system basically three ways:
  1. A decrease in ability to fight infections, tumours and cancer. (poor cell-mediated immunity)
  2. An allergy. (increased sensitivity)
  3. An increased ability to develop autoimmunity.
Industrial chemicals have been linked with an increased incidence of infections, tumours and cancers, allergies as well as auto-immune disorders. How many people in the developed world are coming down with these health complaints? Countless people. Most of these people will have never heard of detoxification or perhaps understand the true value of cleansing the body periodically.

Doctors Don’t Screen For Toxins

My belief is that one of the main reasons why the medical profession views autoimmune conditions as having “no known cause” is that they don’t generally screen for toxins, chemicals or heavy metals in any patient who presents to their rooms with an auto-immune problem.

Cornell University research in 2003 found that almost 40% of all deaths now globally can be related one way or another to environmental toxicity. Auto-immune symptoms are treated with drugs, which masks the real problem, suppresses the symptoms and only adds to the problem of toxic burden.

Environmental toxins 

Conventional medicine does know that auto-immune flares are likely to be triggered by factors such as sunlight, increased stress and some medications.

But – where are all these immune problems coming from? Why does it seem that half of us getting sick with coughs and colds and allergies, and the other half it seems are coming down with an auto-immune problem or cancer? Why?

Western medicine was quite late in figuring out that environmental toxins form an important cause of  immune-related disease, overlooked for too many years. But are they testing for heavy metals and other toxins the patient may have been exposed to? Ask for heavy metal testing at the least next time you visit your doctor. Insist, especially if “no cause” can be established.

Recurring Infections And Poor Immune Response

Apart from several other plausible reasons, I put an increasingly poor immune-response down to two basic things:

1. Stress (we do too much, expect too much, and stress too much)

2. Toxins in our everyday lives & pollution in our environment (currently in excess of 70,000 chemicals exist in our environment).

There are many other potential causes, but stress and toxins appear in my opinion to be two of the largest triggers. The problem with these two big potential causes which arises is that the patient’s stress responses are not recognised or treated in a medical setting, and toxins are rarely if ever considered to be an issue as a contributing factor in the development of any chronic disease, including conditions such as autoimmunity.

3 Toxic Exposure Cases 

1. House renovations

Ruth is in her late 50’s and was diagnosed seven years ago with lupus. About twelve years ago, Ruth completed extensive home renovations, including using a heat gun to remove the old (lead) paint and using extensive polyurethane refinishing on much of the native timber interior. Ruth is also a wine drinker, and enjoys two glasses of red most evenings. When we tested Ruth, we found very high levels of lead to be present along with several mineral deficiencies. She complained of headaches, stiffness and fatigue for almost a year before her diagnosis, and her blood tests revealed quite high anti-nuclear antibody levels.

2. Pest-control gone wrong

A 49yr old farmer came to the clinic after having consulted his doctor, and then referred to a neurologist to be told that he suffers from depression. Jim knew that something was not right, especially once his eyes started to really play up and become blurry and watery for no apparent reason. He came to the clinic complaining of dizzy spells and bad headaches which occurred along with blurry vision. About 15 years ago, Jim used a few different strong chemicals in his house as a pesticide treatment. Over 300 different pesticides are used in my country (NZ), however, some of the products we are using have been banned in other countries because of their toxicity. With our rules lagging behind, these chemicals can turn up in our food.
Jim has never felt well since and now has just recently been diagnosed with a rare auto-immune condition known as myasthenia gravis.

3. Drug induced disease

At least once a week we see somebody with a drug-induced illness. Last week we saw a 22yr old male who visited his doctor complaining of a sore shoulder last year. He was prescribed a powerful anti-inflammatory drug for a few months. After only 6 weeks of taking this drug, the young man developed a condition known as ulcerative colitis.
A co-incidence? Chemicals (household chemicals, agricultural chemicals, pharmaceutical drugs, etc) have a wide range of effects on immune system function.
Studies of thousands of immune compromised patients at the Environmental Health Center (Dallas, USA) have shown that persons with two or more pesticide compounds present in their serum have some form of immuno-toxicity, ranging from a decrease in ability to fight infections and tumours to allergies and autoimmunity.
Currently, studies have shown that genetic predisposition accounts for approximately thirty percent of all autoimmune diseases. The rest, 70 percent, are due to environmental factors, including toxic chemicals, dietary components, gut dysbiosis, and infections.
NZ Ministry of Health studies done in 2001 confirmed that each New Zealander has a minimum of 7 different chemicals in their blood, according to a study involving over 2000 people of all ages in four separate regions in NZ. A 2020 review published online in the New Zealand Medical Journal indicates that a large volume of pesticides used in New Zealand are suspected carcinogens.
Chemicals produced by combustion (car fumes & exhaust emission) have depressing effects on the immune system. Organophosphate (OP) pesticides are still used widely throughout NZ, are toxic to the immune system. They have been found to cause decreased percentages of many different immune cells, and to induce high rates of autoimmunity.
This elevation in autoimmunity is reflected by high levels of antibodies to many different tissues of the body, in addition to elevated anti-nuclear antibody level.(ANA). Similarly, immuno suppression has also been linked to heavy metals in the body. I have found lead, mercury, arsenic and cadmium to be the four main heavy metals which deposit in the body of auto-immune patients, causing problems over time. A Hair Analysis will reveal all.
The notion of chemically-induced autoimmune states is not new, since many chemicals are known to induce for example the onset of lupus. Some chemicals, including formaldehyde are thought to induce tissue-specific autoimmune reactions. Chemically-exposed individuals often present with elevated antibodies to certain body tissues. A study of 298 patients with exposure to industrial chemicals showed that they show either very low activity or very high activity of killer cells (NK), elevated antibodies generally as well as auto-antibodies against their own tissue.

Some immune experts classify auto-immunity as “Immuno-toxicity” and believe that it may be the major factor in the increasing rates of asthma, auto-immune disorders, allergies, cancers, and chronic viral infections world wide. For many individuals, this is basically from living in a more polluted world. Some individuals appear to be less able to clear the daily chemical exposure from the body than others, leading to a total load of toxins that exceeds the ability of the body to adapt. When the toxic load reaches this point, damage to certain organ systems can occur. Next article I will go into more detail about detoxification methods to improve auto-immunity.

Stress and Autoimmune Disease

The best evidence so far for an effect of stress on autoimmune thyroid disease is the well known relationship between the onset of Graves’ disease (hyperthyroidism) and a major stress in a person’s life.
Most of the recent case-control studies have supported stress as a factor that affects the onset and clinical course of Graves’ disease. Because the onset and course of autoimmunity is generally insidious, the effect of stress is often overlooked.
Numerous human and animal studies have demonstrated that psychological and physiologic stressors induce various immune changes.
Stress can affect the immune system either directly or indirectly through the nervous and hormone systems. This is why it is so important for your practitioner to take their time and look at your case longitudinally, i.e.; to go back to see what happened in your life, to see how stress could have affected your health over the years and what were the turning or defining points along the way which preceded the breakdown in your health.
A ten minute visit to your local doctor will therefore generally mean that your diagnosis and treatment will be based rather on your presenting complaints, rather than considering any functional disturbances (adrenal fatigue) leading to the breakdown in your health. In my opinion, appropriate lifestyle changes are extremely important if you want to fully recover from adrenal stress, leading to adrenal recovery.

Stress and Adrenal Fatigue Compromise  Immune Function

Most of the symptoms of auto-immune problems can be attributed to inflammatory processes involving sub-optimally functioning adrenal glands in my experience. The adrenal gland produces a powerful hormone called cortisol which quickly acts to remove and prevent redness and swelling and inflammation of nearly all tissues.

This is the hormone which stops mosquito bites from flaring up, your bronchial tubes and eyes from swelling shut from allergens, and stops mild scratches from becoming what would like you’ve been attacked. Cortisol also helps your liver to release stored glucose (stored energy) which helps you to maintain a smooth even flow of energy throughout the day. That is why many people with auto-immune problems are so tired.
The common identifying factor in most autoimmune diseases is a destructive processes called inflammation which will eventually cause the destruction of cells and tissues specific to the type of auto-immune disease he person has. So how can stress eventually cause an auto-immune condition?
Stress causes eventual depletion of adrenal function, which results in the body’s inability to counter inflammation (poor cortisol levels – your body’s own powerful steroid).
In auto-immune reactions white blood cells attack parts of your body as if they were the enemy, and in most auto-immune reactions the cortisol levels your body produces are inadequate for the degree of reaction taking place in the particular tissues of your body. This is exactly one of the reasons why strong corticosteroids (Prednisolone, Prednisone, etc) are prescribed by your doctor with all diseases involving a very strong inflammatory process, particularly auto-immune diseases. And doctors (and patients too!) love it – the pain goes away like magic.
It is certainly apparent to me that most people who suffer from auto-immunity issues have multiple hormone imbalances including adrenal and thyroid imbalances, yet the blood tests will most often say there is nothing wrong with the thyroid, and also the adrenal glands. In most cases, the adrenal glands need to be optimised first leading to repletion, good energy and eventual recovery.
Adrenal recovery is a process akin to running a marathon. The process can long for some, are you an impatient person? Do you expect results right now ? With correct treatment, many patients will find some improvement in their adrenal health a matter of weeks, some in months, depending on their motivation to improve their health, the degree of pre-existing damage as well as the clinical skills of their health professional.
The healing process can take anywhere from 2 months to 3 years even in the best of hands. I’d like you to bear in mind that auto-immunity is a long marathon, and your recovery should not be expected to be a walk in the park. You will not wake up in a week and be cured remember, it probably took your body a few years of slowly declining health to get here in the first place.
Pace yourself and work on your overall health in small steps, gaining new ground gradually over time. Frustration and disappointments are very common and normal in clinical practice, so don’t beat yourself up please.

Patience is absolutely vital, and during the recovery process, most, if not all, will go through a roller coaster type ride with advances and setbacks.

Don With Rheumatoid Arthritis

Don is a dentist from England originally who came to see me diagnosed with rheumatoid arthritis 6 yrs prior. He is 48yrs old, and when questioned about life before the diagnosis, he mentioned that his business partner’s fraudulent offending 10yrs ago left him bankrupt, his wife left him for his best friend, his dog (a faithful companion for 14 yrs) had died around this time, and his father passed away not long after that.
Each one of these events affected Don, increasing his stress and causing blow after blow to his adrenal glands which became increasingly depleted. With this depletion over the years came the fatigue, less enjoyment in life, recurrent coughs and colds, sleeping disturbances, Don became more irritable and became increasingly more reliant on medications for the many small symptoms, for which his GP prescribed various drugs.
Don did not improve, he now relied on anti-inflammatory drugs to help him through his day with patients, and slowly started to develop pain in his arms and hands. His doctor now prescribed stronger drugs for the pain and inflammation. Still the pain was there, and in fact pain was now causing Don some problems in everyday life; even opening a bottle of pasta sauce became a real ordeal.
After a few years on painkillers, the doctor ordered blood tests and then referred Don to a specialist who prescribed yet stronger painkillers and Methotrexate™, a drug originally designed for cancer patients.
Now let’s go back before Don’s eventual diagnosis, if the practitioner had worked out that he was heading towards burn-out and adrenal fatigue resulting in autoimmunity, measures could have been taken to halt the progression and to reverse his noticeable decline in health & wellbeing.
If Don’s inflammatory blood markers were tested regularly, along with his salivary cortisol levels to assess adrenal function, he may well have recovered before his body’s immune started fighting against itself to create the rheumatoid arthritis condition. Preventative medicine could have saved the patient a tremendous amount of pain and grief, not too mention wasted money and medical resources. I spent about eighteen months with Don all up, and am please to inform that he no longer takes any pharmaceutical drugs, and his outcome has improved considerably to the point that he is back at work and in a much better place. 
Don needed to re-assess his lifestyle early on and make the appropriate changes to prevent such a weakened immune response from happening. This is why preventative medicine is the best medicine, if you have a “feeling” something isn’t right then go to your doctor and insist on testing. 

Has Stress Affected You?

Do you have an auto-immune disease? Think carefully how stress may have affected you over the course of your life time. Did you suffer with events like Don?
Did you have a divorce and property settlement, or perhaps not ever fully recovered from the death of a relation?
Did you get burned with your business, perhaps redundancy or bankruptcy? Were you or are you a working mum or dad, involved day to day with the work grind, worry about paying the bills and have kids? Something may be standing out to you at this point. Go away and think about your reaction to the situation. Your emotional state at the time, what you were “digesting” emotionally can affect you so much more than what you digest nutritionally.
Draw a time line and see how this may correlate with the breakdown in your health and you may see a stress progression. Stay away from the health care professional who does not go into detail about past events which may have contributed to the breakdown of your health. Tell them they are fired.
Diagnosing and prescribing based purely on today’s symptoms is generally a waste of time in auto-immune conditions. The past needs to be assessed carefully, and an appropriate questionnaire will establish how you are today in comparison with the past.

A well structured stress questionnaire can help uncover if your immune system is heading for a crash or not, and your natural health professional can help you.

Auto Immune Disease Diagnosis

There is no “one single test” to diagnose auto-immunity. It is a complex disorder and it can be difficult to diagnose. To assist with a diagnosis, the practitioner should take a full medical history, including any family history of auto-immunity. They should discuss the nature and severity of current symptoms experienced and should conduct a thorough assessment. Blood tests are commonly performed and a urine sample will may also be analysed to check for kidney involvement.
Do you have symptoms and don’t feel satisfied with the diagnosis? Then go and visit somebody else who takes more of an interest in your case.

The ANA Blood Test

The antinuclear antibody test (ANA) test detects the presence of auto-antibodies, this marker can show you to what degree your immune system is fighting your own body. This test is positive for example in 95% of lupus (SLE) cases, and it is important blood test marker to determine many other autoimmune diseases. If the test is entirely negative, then many types of auto-immune diseases are unlikely.
I’ve found that once auto-immunity is diagnosed medically, the case is often closed in the sense that a drug-based regime including pain relievers, hormones, or immune-suppressant drugs are prescribed and usually recommended for the remainder of the patient’s life. Drugs control the symptoms, why establish a cause or help the patient to improve the quality of their life?
It sounds like someone placed the disease in the too hard basket and settled for second best.
Most patients can be helped and improved, some considerably. I never said cure, I said improve, in my experience most  cases of auto-immunity can be improved to some degree, some quite remarkably to the point where the person lives a normal life without medications.
You would be amazed just how good your body can respond to alternative treatments of auto-immune disease.

Autoimmune Disease Testing

What would I do if I had an auto-immune condition? I’d have a food allergy test completed (Elisa test) to determine if I have any food allergies, and probably have a low acid and high alkaline diet. I’d certainly avoid all the known allergenic foods (dairy, banana, eggs citrus, soy, peanut, etc) until I knew they were ok for me. Why have your diet work against your immune system?
The auto-immune diagnosis through your GP and specialist rests on accurate history and physical examination, and high index of suspicion surrounds a backdrop of certain abnormalities in routine laboratory tests – for example, elevated C-reactive protein (hsCRP) as well as the auto-immune specific marker such as ANA (see Part 1 of his series). I’d also have a Hair Analysis completed to check for any heavy metal toxicity (common with auto-immunity) and any mineral imbalances. I will be covering a condition called ulcerative colitis in a future article, and in this bowel related auto-immune condition, I would probably recommend a comprehensive digestive stool analysis (CDSA). They are quite expensive, but generally worth every cent because complex chronic cases benefit so much from pinpointing where the problem areas are. Much more on this later.

Comprehensive Stool Analysis

Dr. Leo Galland

About a hundred years ago, researchers found that people with auto-immune conditions appeared to have bacterial or viral infections. In fact, many researchers today have found this still to be true. A study was published online in 2013  outlines in detail: “The relationships between infections, their main mechanisms and autoimmune diseases. Nonetheless, most of the interactions and mechanisms that influence this relationship are still unknown.”

Dr. Leo Galland from New York was one of the first doctors to find that patients with ankylosing spondylitis have a klebsiella (bacterial) infection in their intestine. Your gut is actually a tube going through the body that is open to the outside environment via the mouth. Because of this, over 60% of the body’s immune system (lymphatic tissues/nodes, immune cells, etc.) resides in your small intestine. A healthy gut provides “surveillance” against all types of bugs and functions as a barrier to prevent passage of foreign particles into your body’s interior.

However, in the case of auto-immunity, there is often intestinal inflammation that challenges this surveillance and then compromises the barrier function due to improper cell to cell junctions lining the gut wall. These improper cell junctions lead to a condition you most probably have heard of this called “leaky gut”, where undigested and potentially antigenic food particles and/or bugs can be released into the blood stream leading to auto-immune reactions.

Additionally, the bowel flora (vital for GI health) is often out of balance or “dysbiotic” creating further challenges for the immune system.
To assess your GI function, stool analysis (CDSA) can be performed which assesses the presence of beneficial bacteria, pathogens, GI inflammation, digestion function, leaky gut, etc. To restore gut function, various treatments are available including amino acids and proper fats to restore gut tissue, probiotics to restore proper flora, herbs and supplements for a variety of mechanisms. See your naturopath!

Read Part 2 of the Autoimmune Disease Series: Autoimmune Disease Treatment


(1)   Stress and Autoimmunity. Tetsuya Mizokami, Audrey Wu Li, Samer El-Kaissi, Jack R. Wall. December 1, 2004, 14(12): 1047-1055. doi:10.1089/thy.2004.14.1047.
(2)   Hicklin JA, McEwen LM, Morgan JE. The effect of diet in rheumatoid arthritis. Clin Allergy 1980;10:463.
(3)   Darlington LG, Ramsey NW, Mansfield JR. Placebo-controlled, blind study of dietary manipulation therapy in rheumatoid arthritis. Lancet 1986;1:236-238.
(4)   Broughton A, Thrasher JD. Chronic health effects and immunological alterations associated with exposure to pesticides. Comm Toxicol 1990;4:59-71.
(5)   Vojdani A, Ghoneum M, Brautbar N. Immune alteration associated with exposure to toxic chemicals. Toxicol Ind Health 1992;8:239-253.
(6)   Selgrade MK, Cooper GS, Germolec DR, Heindel JJ. Linking environmental agents to autoimmune disease. Environ Health Perspect 1999;107:S5811-S811.
(7)   Crinnion, WJ. Results of a decade of naturopathic treatment for environmental illnesses: a review of clinical records. J Naturopathic Med 1997;7:21-27.








Join the Conversation...

Your email address will not be published. Required fields are marked *

Confirm you are NOT a spammer