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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. Patrick Nemechek, D.O. 4 weeks ago

    Yes, the Nemechek Protocol can help a great number of individuals with autoimmune disorders but it requires the rifaximin and vagus nerve stimulation to really change the course of the illness.

  2. Mary 4 weeks ago

    I have read your book, and have a grand daughter on your protocol who seems to be improving. I have Crohns disease since age 12 ( doing great right now with low dose methotrexate and Entyvio every other month). A year ago was diagnosed with RA, but symptoms appeared only once for a period of several days – swollen hands, but then disappeared. My arms and legs are slightly sore from time to time, but I continue to work out at gym several days per week with no pain. Would the Nemechek protocol help me? I already do fish oil and olive oil, just not yet inulin. I lost part of colon years ago from surgery gone bad.. Eager to try it if might help and not hurt.
    Thank you! My daughter started protocol as well as her little one.

  3. Patrick Nemechek, D.O. 2 months ago

    General anesthesia from surgery can trigger or worsen bacterial intestinal overgrowth and I believe this could trigger enough inflammation to activation a pre-disposing gene for an autoimmune disorder.

    So my answer is yes.

  4. Pamela 2 months ago

    My daughter had an amplatzer occluder put in place to close an ASD in 2010 -she was 7 years old, could that trigger an auto immune response ie, increased TPO antibodies, Inflammation? Hypersensitivity reactions associated with
    endovascular devices – just curious as she’s 14 now and has been having chronic fatigue – high TPO antibodies- echo’s always look good – was just wondering if there was an correlation.

  5. Patrick Nemechek, D.O. 2 months ago

    Inulin doesn’t kill off anything.

    It simply reorganizes the gut by increasing the normal healthy small intestinal bacteria and suppressing overgrowth of colonic bacteria.

    It is not absolutely necessary to eradicate Klebsiella especially if a patient is asymptomatic in regards to this organism.

  6. Liz 2 months ago

    Before I take a new supplement I wanted to know if insulin will kill off an overgrowth of klebsiella? I had labs done. I was given GI Microb X to take along with supplements to increase vitamin deficiencies as well as probiotics to increase the good bacteria. I have a lot of food sensitivity and allergies and I get very nervous having to take new things. Any assistance is greatly appreciated. (PS…we are looking at the protocol for our son which is how I got here to your blog. ). Thank you for your time.

  7. Patrick Nemechek, D.O. 3 months ago

    Not that I am aware of.

  8. Anonymous 3 months ago

    Is it possible to stimulate the vagus nerve either directly or indirectly through herbs or medicines like huperzine or mestinon for example? Thank you.

  9. Anonymous 3 months ago


  10. Patrick Nemechek, D.O. 3 months ago

    Yes, it can be very helpful

  11. adele 3 months ago

    Hi Dr Nemechek, I read your book and every one of your article. I would give me a try for my celiac disease ( I believe all diseases are curable and all autoimmune disease are the same ).
    I live in Italy so very far. I would know if a skype consultation can be enough.

  12. Patrick Nemechek, D.O. 3 months ago

    Vitiligo causes the affected skin to loos pigment and become white-appearing.

  13. Rita 3 months ago

    I have 8 yr old granddaughter , ASD, on your protocol for 7.2 weeks. 3 weeks in she developed a sizeable reddened area on the inside of her wrist, with no known trauma. This area turned brown,. 2 weeks later, same hand, she developed 3 reddened areas on top of same hand, which also turned into a dark brown pigment. Her Pediatricians do not know what caused this, or exactly what it is. I know there is a condition “virtiligo” but that causes loss of pigment, white blotches. Could this be autoimmune related condition?

  14. Patrick Nemechek, D.O. 3 months ago

    There is growing evidence that the parasympathetic branch of the ANS must become dysfunctional before autoimmune disorders are triggered.

    There is evidence for this with rheumatoid arthritis and Crohn’s disease and I believe it will hold true for the other autoimmune disorders.

  15. Lilliana 3 months ago

    Can a disfunctiom of the Autonomic nervous system be the cause of Lupus?
    can the protocol help a person with lupus ?
    Been in the full protocol for 2 weeks.
    I am 37. Thank you !

  16. Patrick Nemechek, D.O. 3 months ago

    I would ask your neurologist if their would be any problem with fish oil, olive oil and inulin (a plant fiber found in onions and garlic)

  17. Callie Cooper 3 months ago

    My niece suffers from a rare genetic disease called Batten Disease. As I understand it, she has a build up of proteins and lipids that cause her symptoms (seizures & blindness mainly at the moment). My mother-in-law, who is raising her, seems hesitant to try the protocol. Is this something she could just try and see or does she need to speak with Dr. N before starting?

  18. Patrick Nemechek, D.O. 3 months ago

    Your inclination about the differences is correct.

    Dicyclomine just prevents dyscomfort from cramping and does nothing for SIBO.

  19. Patrick 3 months ago

    Dear Dr. Nemechek-

    I have a 22 year old son with Autism. We are slowly starting your protocol. We have been prescribed Riflaximin by our conventional GI doctor and the insurance company has denied it because it requires a diagnosis of hepatic encephalopathy (HE) or IBS with diarrhea (IBS-D). He has been diagnosed with SIBO (without breath test) and he has constipation and gut pain issues. He has been on Linzess for constipation and now we wanted to start Riflaximin. My question is they want to do dicyclomine instead. What do you feel about this as a substitute? I would imagine they work completely different as one is to eliminate pain and the other kills bacteria. Any insight on what we can do to fight this?

  20. Patrick Nemechek, D.O. 3 months ago

    Not necessarily.

    My adult protocol is very similar to the adult autism protocol I outline in my autism guide.

    We are working on a book for non-autistic adults but it is taking longer than expected because of multiple other time demands.

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