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Triggering Autoimmune Disorders

Triggering Autoimmune Disorders
August 31, 2017 Dr. Patrick Nemechek and Jean Nemechek

Hashimoto’s, Crohn’s, Psoriasis, and Rheumatoid Arthritis are names of common conditions known as autoimmune disorders.

Autoimmune disorders are the result of the dysregulation of the immune system, but why do some people get these disorders when others do not? We now understand how most autoimmune disorders are being triggered by inflammation and Autonomic Nervous System dysfunction.

Autoimmune disorders occur when someone’s immune system spins out of control and targets tissue within their body instead of fighting foreign invaders like viruses or bacteria.

We name the immune attacks by their location in the body.  If the immune system attacks our thyroid, we call it Hashimoto’s thyroiditis.  If the immune attack is in the joints of our hands we call it rheumatoid arthritis.  If the immune attack is against our small intestine we call it Crohn’s disease.  If the immune attack is against our skin we call it psoriasis, or it could be impaired pigmentation of the skin which is known as vitiligo. 


Genes in a Family

The two critical elements required to trigger most autoimmune disorders are (1) predisposing genes within our DNA that is passed to us by one of our parents or triggered by an event such as chemical or radiation exposure, and (2) damage to the Autonomic Nervous System that can occur during our lifetime due to unresolved physical, emotional, metabolic, or inflammatory injuries.

Many people believe that if their parents pass on a gene for a medical condition (diabetes, colon cancer, heart disease), that it is inevitable they will develop the condition.  This is understandable since we often see specific patterns of disease unfold in family histories.

For instance, if someone’s family has several members with diabetes, we know there is a gene increasing the risk of diabetes being passed from parents to child through birth.

But genes must first be activated by something to trigger disease, and it is not inevitable that the gene will always turn on and that the person will develop diabetes.  Many people with brown eyes may also carry a gene for blue eyes which is not yet activated.

I tell my patients to think of the genes in their DNA like breakers inside the electrical boxes in their homes.  If the breakers are in the “off position” someone will not develop an illness.  We now understand an abnormal chemical condition in the body called metabolic inflammation is the primary element that can flip the gene breaker to the “on position” and trigger an illness.


Metabolic Inflammation Triggers Genes

Metabolic inflammation is the abnormal, persistent release of chemicals from the white blood cells called cytokines.  Cytokines should only be released in short spurts, such as when someone has an infection or they are recovering from an injury.  Cytokines are released to fight the infection or repair tissue, then they disappear from the blood stream once the problem is resolved.

When there is metabolic inflammation, however, cytokine production is out of control and it never stops.  And as the levels of the cytokines climb, they begin stressing the cells of the body and ultimately, they are the invisible hands that reach in and will flip the genetic breakers to the “on position”.  This is how most genetically-based diseases such as autoimmune disorders are triggered.


Autonomic Dysfunction Triggers Autoimmune

But there is another piece to the autoimmune trigger process that most people have never heard of.  For someone to trigger genes they might be carrying for any particular autoimmune disorder, they also need to have an unresolved injury to their Autonomic Nervous System. 

I have been testing and treating the Autonomic Nervous System for 11 years and it is clear to me that our modern Autonomic Nervous Systems have become increasingly prone to injury and dysfunction after some accumulation of stress, poor nutrition, vegetable oils in our foods, childbirth, intestinal infections, metabolic or inflammatory events, medications, adverse or excessive reactions to vaccinations, and both physical and emotional concussions and traumas.

The Autonomic Nervous System is the brain’s master control mechanism and communicates with every organ in the body such as the heart, bladder, stomach, intestines and kidneys.  It is how the brain regulates inflammation, the immune system, blood pressure, blood sugar, sleep cycles, and hormones.   

There are two main branches in the Autonomic Nervous System.  In very simple terms, the Sympathetic branch is responsible for energy expenditure (“fight or flight”) and the Parasympathetic branch is responsible for energy conservation and restoration (“rest and digest”).


Autoimmune Disorders and Parasympathetic Dysfunction

These two opposite Autonomic branches should work together simultaneously and in balance but people with autoimmune disorders commonly have dysfunction or weakness in their Parasympathetic branch.  Information from the Parasympathetic branch is carried through the vagus nerve, and has predominate control over inflammation throughout our body.

Dysregulation of inflammation of the Parasympathetic branch is now believed to precede the dysregulation of the immune system seen in autoimmune disorders.

The Parasympathetic branch controls someone’s resting states after a meal and at night, their digestive tract, nutrient storage, immune responses, and healing.  It causes slower heart rates, slows respiratory rates, sleep cycles, gastrointestinal motility, increased peripheral vascular flow, blood flow to cells, liver and kidneys, and venous blood flow return to the heart. 

When the “rest and digest” Parasympathetic brain commands are disrupted, they have a negative effect on the immune system (autoimmune disorders), the intestinal tract (heartburn or constipation), and produce chronic pain syndromes (fibromyalgia).

People with parasympathetic dysfunction often experience sleep apnea, “restless legs”, morning nausea, night sweats or hot flashes, feel power surge sensations when they should be at rest, or experience non-restorative sleep.

The Autonomic Nervous System is very complex network of different areas of the brain, and dysfunction is not as simple as one branch working and the other branch is not.  People with unresolved Autonomic injury very often have symptoms from both Parasympathetic and Sympathetic dysfunction. 

When the “fight or flight” Sympathetic brain commands are disrupted people may also feel tired or chronic fatigue, crave salt or sugar, feel excessively hungry, or feel anxious throughout the day.  People may get severe (“migraine”) headaches, TMJ, heart palpitations, tingling or numbness in their arms (hands or face), disrupted night vision, varicose veins, E.D., stiff necks and shoulders, or insomnia.


Autonomic Testing Detects Dysfunction

The Autonomic Nervous System may be tested by several methods and I prefer non-invasive spectral analysis that can directly measure Autonomic signaling from the brain to the heart.  The results from this test are not just in terms of ‘normal’ or ‘abnormal’, instead spectral analysis testing challenges the branches of the Autonomics and the test results show both Sympathetic and Parasympathetic tone and balance.

The EKG component of spectral analysis Autonomic testing measures heart rate variability (HRV), which is a trace of the intervals between heart beats to within hundreds of a second.  HRV is a function of continuous Sympathetic and Parasympathetic activity, and both these signals are imbedded within the EKG communication between the brain and the heart.

This HRV information is valuable because it reveals if someone’s HRV may be too high or too low as their Autonomic dysfunction progresses, which provides me as their physician the opportunity to first identify and then stabilize the problem. 

There are five stages in Autonomic dysfunction and Autonomic testing may identify preclinical changes even before someone experiences symptoms in Stage 1 or 2.  It is in Stage 3 that people start to experience symptoms that affect their daily life like GI trouble, sleep trouble, headaches, temperature regulation problems, or dizziness.  

Stage 4 and Stage 5 are stages of advanced Autonomic dysfunction and progressively low HRV.  Like Stages 1 and 2, people may also silently slip into Stage 5’s very weak Parasympathetic function and not even realize it.  This very weak Parasympathetic function is also referred to as Cardiac Autonomic Neuropathy (CAN) which has a 50% mortality rate in 5 years if left untreated. 

Although Autonomic injuries seem to be becoming more common in the general population, they are easily detectable and fortunately all five stages of Autonomic dysfunction are now reversible or capable of improvement without long term medications.


Vagus-Inflammatory Reflex

We also now understand that inflammation from the immune system is completely controlled by a process in the brain referred to as the Vagus-inflammatory reflex.  The Vagus Nerve carries information from the Parasympathetic branch of the Autonomic Nervous System, and operates as the regulator of inflammation throughout the entire body.

The signal carried by the Vagus Nerve operates much like your foot on the break of your car.  The stronger the parasympathetic impulse, the more things slow and eventually come to a stop.

Groundbreaking bioelectrical work is being done by stimulating the Vagus Nerve, which has the effect of lowering inflammation.  In order words, stimulation of the Vagus Nerve mimics Parasympathetic signals. 

The ability to lower inflammation via the Vagus Nerve is thought to be so important that it promises to make many medications obsolete in our lifetimes, and it gives us a whole new understanding of stopping disease pathways. 

Implanted devices to stimulate the Vagus Nerve have been done in our country for about 20 years.  I commonly prescribe the use of a transcutaneous (on top of the skin) Vagus Nerve stimulator for my patients, and it has become an important tool in my treatment program, The Nemechek Protocol™ for Autonomic Recovery (Pat. Pending). 

Vagus Nerve stimulation is a complex treatment method and different settings are used for different people depending on their individual health, and are used at varying lengths of time.


Reduce the Triggers of Autoimmune

Knowing that the two critical elements required to trigger most autoimmune disorders are (1) predisposing genes within our DNA that are turned on by metabolic inflammation, and (2) damage to the Parasympathetic branch of the Autonomic Nervous System that is reversible, allows us to act to change our health. 

The key to restoring our natural inflammation control mechanisms is through a reduction of inflammation throughout the brain and body by using every scientific, nutritional, and bioelectric tool available.

I am an internal medicine physician (D.O.) from UCLA and my Internal Medicine and Autonomic practice is in the Phoenix area. I use a variety of methods including Vagal Nerve stimulation, and I have discovered a multifaceted formula for Autonomic Nervous System restoration that is so groundbreaking that I filed a patent application for The Nemechek Protocol for Autonomic Recovery (Patent Pending).

I have also published The Nemechek Protocol™ for Autism and Developmental Delay at

For additional information, call my office 623-208-4226 or go to

This post is provided as an information resource only, and is not to be used or relied on for any diagnostic or treatment purposes. This information is not intended to be patient education, does not create any patient-physician relationship.

© 2017. Nemechek Consultative Medicine. All Rights Reserved. Patent Pending.


  1. Kristin 1 month ago

    Dr. Nemechek, I am wondering if the cytokine storm created by mycotoxin exposure through toxic mold in the home would also lead to the ANS dysfunction? We have successfully completed the Shoemaker Protocol post toxic mold exposure, but the gastrointestinal issues and food sensitives have not subsequently resolved. I see that mold exposure is not listed on your list of inflammatory injuries and am wondering if your patients who do not have their inflammation come down may be having current exposure to mycotoxins in their homes. Is this something you have run into with any of your patients? Would your protocol work post treatment for mold exposure to resolve the remaining issues with the gut? Also, for patients that have any kind of medical device (like medical mesh, joints, implants etc.) that are creating continuous inflammation (my husband has a hernia repair), would this protocol still work or if the source of the inflammation cannot be removed from the body, would the ANS never repair? Would you just recommend more fish oil for those category of patients?

  2. Patrick Nemechek, D.O. 1 month ago

    If an individual has pre-existing primed microglia from bacterial overgrowth, diesel fume exposure, recurrent traumas or prior CNS infections for example, then any spike in pro-inflammatory cytokines can result in chronic autonomic dysfunction.

    The protocol is capable of overcoming the cumulative inflammatory levels in the majority of my patients including those with autoimmune disorders and prosthetic implants.

  3. Anonymous 1 month ago

    Hi Dr. Nemechek,
    Is your protocol capable of reversing autoimmune disorders or just sort of easing symptoms?
    My son has been on your protocol for several months now with good results, now just waiting for him to really “catch up” – I suspect this will take a few years because his brain is still not “healed” but we are trying to be patient. I hope to have this type of success with my husband’s joint pain as well.
    Thank you!

  4. Patrick Nemechek, D.O. 1 month ago

    Theoretically, the goal is to lower pro-inflammatory cytokines to such an extent that the genes involved with a particular disorder (diabetes, high blood pressure and autoimmune disorders as examples) literally shut off and the disease process stops.

    This has been demonstrated to be possible in animal models but I am uncertain if we are able to prove this yet in humans.

    That being said, this protocol can greatly reduce the symptoms associated with autoimmune disorders and I have had a number of patients with a variety of autoimmune disorders seemingly go into remission (multiple sclerosis, ankylosing spondylitis, psoriasis and Hashimoto’s).

  5. Eunice 1 month ago

    Hello Dr Nemechek! I’m happy to hear about your protocol and successful cases and I read your book and got to understand how important our gut when it is healthy. I’m a 41 years old lupus patient. Do you think I can see hope and miracle in this protocol? I started this protocol a month ago with up to 2 teaspoon of inulin, 6 capsules of fish oil (but other brand which I’ve been taking more than 2 years), and extra virgin olive oil (a well-known brand in Greece) in my daily home cook meals. I had a few nights of insomnia in the second week. After that, I started to see oil in my stool and then urine. Is it caused by excess intake of fish oil? I took vitamin supplements at the same time with this protocol, should I drop the supplements (b-complex, E, garlic, turmeric, calcium, vitamin D, magnesium, coQ-10, multi-vitamins with mineral)? What happened to my stool and urine with oil? I’m quite scared of seeing the oil in the toilet bowl. I’m still taking my medicines that prescribed by my (lupus) physician here in Malaysia — levothyroxine (hypothyroid), hydroxychloroquine, prednisolone (my low platelet count). So now, should I continue my 2 teaspoon of inulin? What about fish oil? I’ve bought the Now brand fish oil but I haven’t started it because I stop taking fish oil these 3 days after seeing the oil in the toilet bowl. I hope to get your reply soon. Thank you and god bless.

  6. Marisa 1 month ago

    Where can I find your protocol? I have ankylosing Spondylitis and live in St. Louis.

  7. Patrick Nemechek, D.O. 1 month ago


    You case is very complex. You could learn more about how I approach these problems with a one-on-one Skype session. More info can be found under the About tab at the top of the page.

    Dr. N

  8. Patrick Nemechek, D.O. 1 month ago

    A copy can be purchased at

  9. Kristin 1 month ago

    I have seen you mention the mast cell response when you have been talking to patients having histamine reactions to the fish oil. I assume based on what you have written that you are quite familiar with mast cell diseases. One of my daughters has systemic mastocytosis. Her tryptase is above 20 and she has high histamine levels, but we never ran the bone marrow biopsy to check for the KIT gene mutation. Based on what I think I understand from reading your book and blog, people who have mast cell destabilization secondary to an inflammatory response, be it from an environmental injury or otherwise, would have a chance to recover through the protocol by healing the gut, bringing down the inflammation and allowing the ANS to self repair. I would like to share your blog and book with some of the mast cell boards that I frequent, where patients and parents share what is working for them. Before I do that, have you treated any patients with mast cell diseases like MCAD, MCAS, or systemic mastocytosis? Have they seen improvement on this protocol? Would you think that disease process would be as apt to recover as the autoimmune diseases you mention in the blog above? Would you think that as long as it is not the genetic form with the KIT mutation that it could actually reverse? Do you think even those with the KIT mutation might benefit? I ask because I saw you answer a parent about cases of Autisim not fully recovering when there was an underlying genetic disorder (like fragile x) so I assume the same may be true in other arenas? I have put my daughter on the protocol, but not introduced the fish oil yet as she has had mast cell reactions to that in the past with cortisol/adrenaline dumping. I am hoping by allowing the inulin to go for a while that she may better tolerate it in a few weeks. I would like to share your wonderful information and just wanted to ask those few questions before I did. Thank you for all your amazing work!!

  10. Patrick Nemechek, D.O. 1 month ago

    I have treated patients with a variety of mast cell disorders and the majority benefited greatly.

    I can’t really comment on my protocols effectiveness against the KIT mutation specifically.

  11. Shannon 4 weeks ago

    My son is 16 and has autism, secondary to a chromosome abnormality which he inherited from me. I have not been affected by it, so it leads me to believe that something happened to him, perhaps a metabolic injury, that did not happen to me. After reading so much of your blog
    , I can see that I (and other relatives) most likely have autonomic dysfunction since I relate to so many of the symptoms you describe including POTS.
    I believe my son has been autistic since birth. Is it possible that he acquired autonomic dysfunction in utero? And would it still be possible to turn his genes off with this protocol?

  12. Patrick Nemechek, D.O. 4 weeks ago

    I believe it’s all possible.

    I also believe the chromosome anomaly may have nothing to do with his autism since it didn’t affect you in that way.

  13. Fiona Grant 5 days ago

    dr nemechek, I need to buy some powered inulin (I have your book and have read most of it) and was wondering exactly which brand of inulin I should buy? I live in Australia but could buy online. kind regards Fiona

  14. Patrick Nemechek, D.O. 5 days ago

    I prefer using inulin produced by NOW Foods.

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