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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. Sarah Brant 2 days ago

    Hi Dr N!

    I started your protocol in July, about the same time I had my thyroid medication adjusted. My free T4 was in the optimal range but my TSH was super low at 0.0058. I was taking 50 mcg of levothyroxin. My Dr told me to drop one dose per week to hopefully bring my TSH up above .4. I just had levels rechecked and amazingly my free T4 was .99 and my TSH was 3.15. I don’t feel great. My Dr was very surprised. I’m now going back up to 7 days per week dose for two weeks and then after that he wants me to start taking my dose 13 out of 14 days and see what happens. I’m curious to know
    If the protocol using inulin could have somehow affected the situation with my thyroid. I realize that to achieve true recovery I need rifaximin. I guess I’m just wanting to make sure that I’m not making it worse with inulin. I’m new to the world of thyroid issues, I was diagnosed in Dec.. Thank you!

    • Patrick Nemechek, D.O. 1 day ago

      Inulin and rifaximin both could improve absorption of your thyroid medication.

  2. Jordan 1 week ago

    Hi Dr. Nemechek,

    I have been on your protocol for 3 months and have done 1 round of Xifaxan so far. Thank you for your work! I have Chronic Lyme disease and was diagnosed with SIBO in Nov 2017. My health went into a fast & furious downward spiral after the birth of my 3rd child in 5 years. My most pressing issue is severe swollen lymph nodes in my neck every time I eat. It started in Nov 2017 with just a few foods. I went gluten free, dairy free, soy free & sugar free.

    But the lymph node issue has only gotten worse, and I now react to everything I eat. I was originally thinking it was related to leaky gut/SIBO/some sort of autoimmune thing and was hoping to see improvement with the Xifaxan, but I didn’t.

    So my question is, do you think continuing your protocol will eventually fix the underlying issue causing my swollen lymph nodes? Is lymph swelling associated with Autonomic Dysfunction? Also, I’m a 28 yr old female. If I made an in-person appointment, would I be guaranteed to get the VNS?

    • Patrick Nemechek, D.O. 1 week ago

      I’m uncertain of a mechanism to cause sudden swelling of cervical LN after eating.

      No one is every guaranteed anything except a visit to me and a customized treatment plan that best suits their situation.

      Clinical medicine for chronically ill, complicated patients is far more complicated that many people envision.

      We routinely tell people on the phone to not make an appointment if they are anticipating this or that treatment strategy from me.

  3. Amy Tanner 2 weeks ago

    So I have been on the protocol for about a month now including rifaximin. I have Crohn’s disease and some anxiety issues. I have recently started taking the chicory root inulin after finishing the rx to help with stomach issues and I think it’s helped. I was just diagnosed with Pneumonia last night and had to have a steroid shot, two antibiotics (because I can’t take the one they wanted me on), methylprednisone steriod pack, and an inhaler. Ahhhhh! I did get the urgent care dr to rx me another round of rifaximin for afterwards. My question is since undoubtably these medications will send me into a relapse, how long after finishing the antibiotics should I start the next round of Rifaximin? And can I continue the inulin during antibiotic treatment? Once I start rifaximin again should I stop inulin? Thank you so much for all the work you do! It’s been so wonderful for our family!

    • Patrick Nemechek, D.O. 2 weeks ago

      Antibiotics don’t always cause relapse but if they do you’ll often experience a return of the symptoms that went away within the 2 weeks after finishing your first round of Rifaximin.

      Generally the inulin doesn’t seem to help much after rifaximin and doesn’t seem to prevent relapse. But inulin is pretty harmless stuff and if it seems to help in some way, its fine to continue it.

  4. Erika 2 months ago

    Hello Dr. Nemechek:
    First, thank you. My entire family has been on your Protocol since February!
    I’ve been speaking with my cousin about your Protocol at length. She is in her early 30s and has several health issues, including an autoimmune disorder which causes cysts. She has a history of c diff, but it is not showing active symptoms right now. She has recently started the EVOO and fish oil. She removed oils high in omega 6 quite a while ago (she’s been on a paleo AIP diet to help control the autoimmune issue). She spoke with her doctor about getting the Xifaxin. The doctor is suggesting a shot instead of the pills. Would this be an acceptable alternative, or should I urge her to request the pills instead? Thank you!

    • Patrick Nemechek, D.O. 2 months ago

      I do not know of any shot that could replace the impact of Xifaxan (rifaximin)

  5. Mom 2 months ago

    My 4 year old son was diagnosed with autism when he was 2.5 and then PANS when he turned 4 by a positive CaM Kinase II on the Cunningham Panel (none of the antibodies on the panel were elevated). I discovered your protocol right before his diagnosis of PANS. I started in February 2018 on the full protocol. He was on antibiotics and five days of prednisone from end of April until mid June. My issue is he’s always had a very mild eye tic, it went completely away in June, now it’s back worse than ever with his neck jerking and a vocal tic. He’s on all recommended brands and dose for his age with no other meds or supplements. Can you give me any insight into why his tics have increased or how to stop them? They’re very noticeable and obvious. His pediatrician thinks maybe he needs another steroid burst thinking the tics are PANS related, but I’m hesitant to restart a burst or antibiotics. He’s had a gamut of labs and there’s no known bacterial/viral cause for his PANS.

    I just want to stick to your protocol and hope these tics go away, but with school starting soon I do worry. His autism behaviors have greatly improved since February. In June when his tic was gone was the first time I think he could pass as a totally neurological child. Now with these intense tics and increased defiance/OCD, I’m feeling confused. Thought I’d go straight to the source for an answer. Thank your Dr. Nemechek.

    • Patrick Nemechek, D.O. 2 months ago

      The frequency and intensity of tics seem to be related to the extent of bacterial overgrowth. I focus on increasing the dosage of inulin to improve the control of tics.

  6. Patricia 2 months ago

    Dr. Nemechek,

    We have a nine-year-old son who may be on the spectrum. We have your book and have been on the protocol since February. He has always been a poor eater and we have always attributed it to constipation. We stopped giving him psyllium as per what we have read from you and started giving him CALM, magnesium supplement. It isn’t as effective, and he continues to struggle periodically. Is it alright to have him drink kefir or any other form of natural probiotic in his diet?

    • Patrick Nemechek, D.O. 2 months ago

      I am against the use of any probiotic.

      Constipation is due to autonomic dysfunction (its a brain issue) and recovers slowly over a few months. I don’t know exactly what a “poor eater” really means so I cannot comment on this but to say many kids who have a limited range of foods they are willing to eat (“picky eaters”) will often just start eating a wider variety of foods after several months on the protocol.

  7. Deanna J Hamilton 2 months ago

    Dr Nemechek, I have just recently started your protocol for my daughter who is ADHD. While researching for her i was recently diagnosed with Hidradenitis Suppurativa which as explained to me is an auto-inflammatory disease. Have you had any patients you have treated with your protocol with HS? Or do you think due to the inflammatory processes with this disease it would be successful on your protocol? It has been very painful over the last few months and I believe it has increased due to recent surgery and being placed on antibiotics which may have not been necessary. Thank you for your input!

    • Patrick Nemechek, D.O. 2 months ago

      The protocol does seem to help HS but I haven’t seen a complete recovery nor tried the use of VNS as part of the protocol for this.

  8. Linda Allebach 2 months ago

    I have had numerous autoimmune disorders (IBS, Ankylosing Spondylitis, Alopecia Areata, Iritis [both eyes at once], Psoriasis). Strong gene disposition from mother’s side of GI dysfunction, RA, and Scleroderma – that I know of. Changed my diet to the Specific Carbohydrate Diet (SCD) and most IBS problems are pretty easily managed; essentially it’s no grains, no starches, and no sugars except a little honey. Starting my 9th year in October, so yes it’s been a long journey. Make most food from scratch but find more and more online vendors manufacturing SCD “legal” items and am very grateful. Believe my basic problem was SIBO and is made worse by antibiotics, other drugs (have had severe reactions to them and antiemetics). Hope to stay away from pharmaceuticals as much as possible and been successful so far. Lately have a problem with heartbeat – most likely A-fib but echo cardiogram shows structure is fine; another functional problem. Thinking about the Vagus nerve and wondering if that’s connected to, like everything IS with autoimmune… Unfortunately, over the years I found no medical help really but always KNEW these varied and seemingly unrelated illnesses were connected. Could never find a doctor to help me with this idea. So I wanted to share this and encourage you to research the SCD – probably the only reason I am still alive at this point and can have as close a “normal” life as is possible in my situation.

  9. Rosemary 3 months ago

    Hi Dr. N
    My son has severe Crohn’s and is doing many things to stay ahead of it.
    Since he is a strict organic non-gmo vegan, which fish oil can he soncume?
    Thank you for any advice.

    • Patrick Nemechek, D.O. 3 months ago

      I haven’t had any success with patients using vegan omega-3 supplementations.

      You should search for the papers discussing the success of rifaximin in Crohn’s disease. A 10-day has the potential of triggering remission in 45-60% of patients.

  10. Mary 4 months 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.

    • Patrick Nemechek, D.O. 4 months 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.

  11. Pamela 5 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.

    • Patrick Nemechek, D.O. 5 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.

  12. Liz 5 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.

    • Patrick Nemechek, D.O. 5 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.

  13. Anonymous 6 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.

    • Patrick Nemechek, D.O. 6 months ago

      Not that I am aware of.

  14. Anonymous 6 months ago


  15. adele 6 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.

    • Patrick Nemechek, D.O. 6 months ago

      Yes, it can be very helpful

  16. Rita 6 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?

    • Patrick Nemechek, D.O. 6 months ago

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

  17. Lilliana 6 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 !

    • Patrick Nemechek, D.O. 6 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.

  18. Callie Cooper 6 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?

    • Patrick Nemechek, D.O. 6 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)

  19. Patrick 6 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?

    • Patrick Nemechek, D.O. 6 months ago

      Your inclination about the differences is correct.

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

  20. pallavi mehta 6 months ago

    I would like to go with your treatment. But I live in India.
    Do I have to visit buckeye?

    • Patrick Nemechek, D.O. 6 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.

  21. pallavi mehta 7 months ago

    Hi Dr. Nemcheck,

    I have been suffering from autonomic dysfunction for the last 5 years. It started with dermatitis on my scalp which is nothing but neurogenic inflammation caused by some dysfunction in the sympathetic branch. Then I started getting more diseases like psoriasis, IBS, Ulcers, hot flashes, insomnia, fatigue, less periods, bone thinning, skin thinning, stretch marks etc
    3 years ago I started doining meditation and I noticed the very second day that my psoriasis was gone then I stopped doing meditation, psoriasis came back and then started doing meditation again then again psoriasis went back. So I think these autoimmune diseases have with sympathetic nervous system and not parasympathetic.
    I also read a study that said people with psoriais have a sympathetic dysfunction. so, vagus nerve stimulation will only control symptoms because when we stop doing it then the symptoms will come back right?
    Because the main underlying problem is with sympathetic branch.

    • Patrick Nemechek, D.O. 7 months ago

      Patients with psoriasis or any autoimmune disorder have significant parasympathetic damage in addition to sympathetic dysfunction.

      Vagus stimulation alters immune function via both the parasympathetic and sympathetic branches.

  22. Anonymous 7 months ago

    Hi Dr Nemechek!
    This protocol can help vitiligo? Do you have patients that help their vitiligo?
    Thanks in advance

    • Patrick Nemechek, D.O. 7 months ago

      I have seen vitiligo in some adults improve.

  23. Vicky Garcia 7 months ago

    Would you recommend the vagus nerve stimulation to help the motility?

    • Patrick Nemechek, D.O. 7 months ago

      The use of VNS is based on age more than symptoms

  24. Vicky Garcia 7 months ago

    Thank you very much for your response

  25. Vicky Garcia 7 months ago

    Hi Dr Nemcheck, i recently purchased your book The Nemcheck Protocol and have a question. I have an 8 year old son born with chronic intestinal pseudo obstruction. He has very slow motility in his small bowels but decent motility in the colon. He has very bad bacterial overgrowth. Can he use inulin with slow motility ? He has a gtube used for venting and an Ileistomy.

    • Patrick Nemechek, D.O. 7 months ago

      chronic intestinal pseudo obstruction is commonly associated with bacterial overgrowth as well as autonomic dysfunction. Both of these components are improved with The Nemechek Protocol.

      I think the prebiotic effect of inulin might be very useful. The fish oil and olive oil would as well. The key would be to start at low doses and increase slowly.

      I would discuss this with your physicians beforehand.

  26. Elsa 7 months ago

    Thank you so much!!!

  27. Cristina Acosta 7 months ago

    Hi Dr. Nemechek! How long do you wait to repeat a round of antibiotic?

    • Patrick Nemechek, D.O. 7 months ago

      Only if there are signs of SIBO relapse.

      SIBO relapse tends to mimic the original symptoms but in reverse.

      If diarrhea or heart burn from tomatoes resolved with rifaximin, then diarrhea and heart burn from tomatoes returns.

      I recommend a repeat treatment every 18-24 months in my long term recovery patients

  28. Shannon 8 months ago

    I’m a hashimotos patient who has a horrible histamine response. In your book you say it’s directly related to SIBO. My Dr gave me the antibiotic script but it will cost me $450 each time I take the 550 mg x2 for 10 days.
    I’m concerned about how many rounds of antibiotic I will need as $450 is so pricey.
    * on avg how many rounds do your autoimmune patients take to start to see major gains in histamine issues?
    I know I can’t take inulin after a round of antibiotics.

    • Patrick Nemechek, D.O. 8 months ago

      If you don’t try to fix autonomics, the relapse rate can be every few months.

      My patients who experience autonomic recovery often rarely need repeat treatments.

  29. Anon 8 months ago

    Dr Nemechek, what do I when my husband is not on board? He has so many issues and takes more than 10 supplements and meds. Not only it’s a waste of money, but obviously it’s not working. He’s very obese as well. One time I told him to stop buying men’s multi vitamins but today I saw it again. I feel all the cost associated with fish oil and inulin is waste for him. I already showed him the book but don’t get the feeling that he read it. In the mean time, my ASD son is doing better but not enough to convince my husband.

    • Patrick Nemechek, D.O. 8 months ago

      Focus on the child and hopefully your husband will take serious notice.

      Unfortunately, you can lead a horse to water but…

  30. Shannon 8 months ago

    Thank you for all that you do! My son has been on the protocol for almost a month and I see amazing changes in him. He was recently diagnosed with ADHD and sensory processing disorder. I am so thankful for your wisdom and work in this field. My question is for my husband. He doesn’t have major bowel issues, but when stressed he tends to get sicknesses (colds) more often and/or he has bouts of diarrhea when stressed. Since you are located in AZ we are not local to you, and I am hoping inulin will help him. He started on 1/2 tsp with the recommended dose of inulin, he takes Nordic naturals omega 3 and California ranch omega 9… he feels ok, but gassy. Regular bowel movements 1x/day . IS the gassiness ok? Should he push through or is this a sign he may need to antibiotic or to cut back? When do you KNOW that your body is working as it should on this protocol?
    *I have hashimotos and I am on it too!
    * I just bought the book- yay

    • Patrick Nemechek, D.O. 8 months ago

      Gassiness is harmless and generally indicates there is a little too much inulin passing into the colon.

  31. Sandy 8 months ago

    What vegetarian approach do you take if you cannot tolerate fish oil pills?

    • Patrick Nemechek, D.O. 8 months ago

      I don’t know of one that provides enough DHA omega-3

  32. Anonymous 8 months ago

    Thank you.

  33. Anonymous 8 months ago

    Hello Dr. N,
    I am in remission from Lyme 2 years but still battle with gut issues. Last year January 2017 I had a bad bacteria overgrowth Citrobacter Freundii which took me several months to get rid off. I read that FOS feeds it. Are Inlulin and FOS the same thing? I see them interchangeable. So I have stayed away from that particular prebiotic fiber but have used others. Would it be ok to start Inulin with that past history? It was a nasty one and don’t want to get again but also want to heal my gut.

    Thank. you.

    • Patrick Nemechek, D.O. 8 months ago

      If you believe you have bacterial overgrowth and are afraid of inulin, then I recommend considering rifaximin.

      Inulin by the way does not “feed bad bacteria” in the small intestine.

  34. christi a fieselman 8 months ago

    I guess I should wait for the autonomic recovery since my daughter is suffering greatly from pots and possible mast cell issues.. How long before it gets out?

    • Patrick Nemechek, D.O. 8 months ago

      A few more months but reading the book on autism will tell you how I address autonomic dysfunction in kids.

      Autonomic dysfunction occurs through a mechanism called cumulative brain injury.

      A copy of the autism protocol can be purchased at

  35. Ann's Mom 8 months ago

    Hello Dr. N,

    I have taken the autoimmune disorder quiz and i did fall under that category.
    I have an autistic 7 yr old for whom we are following your protocol-Inulin,omega-3s and olive oil and she is making decent progress. My question here is, will a course of Rifaximin help in reversing my intestinal imbalance for good, if taken along with omega 3s and olive oil? I plan to get pregnant in a few months- I want to lessen the chances of having one more kid on the spectrum. Please give your suggestions. Thank you !

    • Patrick Nemechek, D.O. 8 months ago

      I’m glad to hear your child is improving on the protocol.

      I discuss the issues of prevention in my protocol guide.

      A copy can be purchased at

  36. Farjana Rahman 8 months ago

    Hello Doctor :

    I jhave just completed reading your amazing book and want to start your protocol ASAP. I have question for you though before start. My 4 year old son who was recently diagnosed ASD is taking magnesium, iron, and melatonin on a daily basis for having sound sleep. Do they conflict with the protocol? Please advise.

    • Patrick Nemechek, D.O. 8 months ago

      Not necessarily but if my patients don’t see much improvement I ask them to discontinue all supplements in case some are preventing recovery.

  37. Shara 8 months ago

    Dr. Nemechek…Thank you for being accessible as you are so busy. I am reading your book. I am 53. and I will be Skyping with you in Feb. in the meantime, I am in California is there a lab test I can get to show bacterial over growth? I have heart burn and I feel dysbiosis/motality is a culprit like you discuss in your article And I’m wondering if I need to get a prescription of Rifaximin too? I can’t wait for our meeting.

    • Patrick Nemechek, D.O. 8 months ago

      There is a breath test for bacterial overgrowth but it is very inaccurate and often poorly performed.

      You’ll need to get a physician to order the medications and any testing for you because I can only order those after a face-to-face visit in Arizona. Because of licensing regulations, I am unable to do so after a Skype session, these are purely educational.

  38. Kari Reinhardt 9 months ago

    Dr. Nemechek, I heard about your book/protocol on an autism facebook group a few days ago and read it in one night. Your work is extremely interesting and I appreciate you making it so accessible and affordable. So thank you for that. Our 7-year-old autistic son has been on a bio-med protocol for close to a year now (GFCFSF and sugar free) and he’s made significant progress with the exception of his gut. He began to have constipation issues after weaning him from breast milk at 1.5 years and although things are moving now with the help of Magnesium, his gut is still very sick. Interestingly, the three steps in your protocol were also listed as recommendations after all the tests he went through, but were never considered priorities. So we are going to start him right away on the Nemechek protocol since it’s significantly easier than going further with the diet to SCD or GAPS. But I have a couple of quick questions. Can we used refined coconut oil? We already use refined because it’s hard to have everything taste like coconut. My next question pertains to me. I believe in my heart I passed my gut issues on to my son. I’ve had IBS since I was very young, and he and I have many similar gut issues. I have also now developed arthritis which is making it hard to do the things I need to do each day. I’m going to start the protocol as well, but do I need Rifaximin then rather than inulin? How likely is it that my primary doc would prescribe for possible SIBO? And if you do use Rifaximin, do you then take inulin daily? And thank you again for putting this information out there for us parents. It’s worth a shot and there is literally no down side to trying.

    • Patrick Nemechek, D.O. 9 months ago

      Coconut milk is not required with my protocol, and be certain that you do not continue the probiotics after starting either inulin or rifaximin.

      We adopt our mother’s intestinal bacterial blend at birth, and very often additional damage is done to the child’s gut bacteria in the first 12-18 months in order for autism to occur.

      My adult patients all require rifaximin to reverse bacterial overgrowth enough in order to reverse chronic brain injury (the primary focus of my research).

      After taking rifaximin, the continued use of inulin doesn’t seem to help prevent relapse and sometimes can cause bloating or flatulence.

  39. Tammy Gipson 9 months ago

    Hi Dr. Nemechek. I met someone today that sent me to search about you. I am a 46-year-old female that was diagnosed with thyroid cancer in 2013 and had a total thyroidectomy. I struggle daily with my energy or should I say ‘severe lack of’ as well as my skin is dry, weight, lethargy, brain fog and so many other symptoms. This has become my new ‘normal’ after the surgery. I am on Synthroid 175 and Cytomel 15 each day and some days I feel fine and other days, for no reason, I’m so lethargic and absent-minded that It’s hard to function. I was wondering if you felt that you could help me?
    Thank you for your time,
    Tammy Gipson

    • Patrick Nemechek, D.O. 9 months ago

      Autonomic dysfunction becomes more and more likely as a cause of symptoms in patients as more and more doctors seem unable to find a cause for the symptoms.

      If that case fits you, then yes it is very likely I can help you.

  40. Fiona Grant 10 months 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

    • Patrick Nemechek, D.O. 10 months ago

      I prefer using inulin produced by NOW Foods.

  41. Shannon 10 months 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?

    • Patrick Nemechek, D.O. 10 months 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.

  42. Kristin 11 months 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!!

    • Patrick Nemechek, D.O. 11 months 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.

  43. Marisa 11 months ago

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

  44. Eunice 11 months 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.

    • Patrick Nemechek, D.O. 11 months 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

  45. Anonymous 11 months 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!

    • Patrick Nemechek, D.O. 11 months 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).

  46. Kristin 11 months 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?

    • Patrick Nemechek, D.O. 11 months 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.

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