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Nemechek Protocol For Autism

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Nemechek Protocol For Autism

The Nemechek Protocol has helped many children with autism who have SIBO infections along with homeopathic support.
Contact us to learn more!

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This Protocol is designed to help to eradicate SIBO (Small Intestine Bacteria Overgrowth) that is so common in children with autism, ADHD and other developmental diagnoses. It helps to reverse the damage being done to the Autonomic Nervous System. This disturbance is connected to other issues related to SIBO.

The Nemechek Protocol requires a daily dose of

  1. Inulin

  2. Omega 3's

  3. Olive Oil

  4. STOP any probiotics while on this protocol

Inulin Dosing Instructions

Gummies: recommended dose is 2-4 gummies a day

  • Start low and go slowly.

  • The recommended brand of Inulin gummies is Fibre Choice Fruity Bites

  • each gummy has 1.5 grams of Inulin fibre.

  • Inulin can cause stomach pain, painful gas, bloating and constipation.

  • Once you see the signs of “awakening” - more alert, more engaged etc. - you can hold at that dose for a while.

  • Once you see the awakening you know that the inulin has done its job and now you need to focus on the omegas.

Inulin Powder: recommended dose to start is 1/8 to 1/4 tsp. 1 - 2 times per day. If not reacting, work up 1/2 tsp. - 1 tsp. of Inulin powder. (See page 40.)

  • The recommended Inulin powder is made by NOW brand.

  • It is flavorless and can be added to beverages or hidden in food.

  • Avoid the ones with added probiotic or digestive enzymes!

  • Larger children (and adults) can safely go up to 2 teaspoons per day.

  • Beyond that amount Dr. Nemechek says he has not seen any additional improvement, and it just seems to cause too.

  • There is no preferred time to administer the Inulin though some people prefer to give it in the morning so that any uncomfortable bloating or gas pains settle before bedtime.

  • The inulin usually results in an increase in awareness and activity within a few weeks.

  • NOTE: If children have difficulty with diarrhea or prior problems with fish oil causing diarrhea, have them start the inulin fiber alone for 2-3 weeks in order to let the gut bacteria balance out. Then slowly increase the dose of fish oil so tolerance is much better.

NOTE: If children have difficulty with diarrhea or prior problems with fish oil causing diarrhea, have them start the inulin fiber alone for 2-3 weeks in order to let the gut bacteria balance out. Then slowly increase the dose of fish oil so tolerance is much better.

OMEGA 3 (Fish Oil) - only recommends Now or Nordic Naturals for this

Note: Cod liver oil works well, dose in same manner.

The Omega reduces inflammation.

  • Kids: Start at 600 mg per day (2 gummies) if kids won't take other oils

    • The recommended brand of Omega 3 is Nordic Omega-3 Fishies (made by Nordic Naturals).

    • Kids need 600 - 1000 mg per day.

    • Omega 3 fish oils: 0 - 6 months old 150 mg, ages 7 - 12 months 300 - 450 mg; ages 1 - 5 is 450 - 600 mg; ages 5 - 7 is 600 - 1000 mg; ages 8-10 1000 - 1500 mg, ages 11-14 1500 - 2000 mg, ages 15 - 18 2000 - 3200 mg; Older than 18, must contain 3000 mg of DHA (see page 54 of book)

    • Increase the daily dose of omega-3 fatty acids from 600 mg per day for younger, smaller children up to a total of 3,000 mg (total of EPA and DHA) depending on weight.

    • The fish oil should have some impact on neurological development within 4-8 weeks.

    • If none is seen at this point, increasing the fish oil is a good next step.

    • The recommended brand of Omega 3 is Nordic Omega-3 Fishies (made by Nordic Naturals).

    • Cod liver oil is allowed as long it has  )

    • When in doubt favor a high dose.

    • If your kids do not like the gummies any high quality liquid fish oil will do as long as it contains DHA & EPA.

    • DHA can penetrate the brain.

  • Adults: Slow increase the daily dose to 3000-4500 mg per day (6 capsules) in teenagers and adults.

    • Adult brand is NOW foods brand DHA-500.

    • There is no preferred time of the day to administer the Omega and it can be given at the same time as the Inulin.

    • Many benefit from waiting two weeks after starting the Inulin before adding in the Omega 3.

    • However, if you or your child)were already using Omega 3 there is no need to stop and wait 2 weeks.

    • Just keep taking the Omega 3 as you were and add in the Inulin.

    • Please avoid products that are Omega 3-6-9!! You want to avoid Omega 6 because it is inflammatory!

OLIVE OIL (Oleic Acid)

  • This helps reduce inflammation. Use it whenever possible.

  • The recommended brand to use will be found at California Olive Ranch Extra Virgin Olive Oil (EVOO)

  • The daily recommended dose is:

    • Children less that 5 years old, using EVOO when cooking foods should be an adequate amount.

    • Starting at age 5, in addition to cooking with EVOO, patients are given the following guidelines:

    • Age 5 - 10 years, consume 1/2 a tablespoon a day.

    • Age 11 -18 years, consume 1 tablespoon per day.

    • Age 19 years and older, consume 2 tablespoons per day. It is a natural oil and healthy for anyone!

    • Cook with olive oil daily and if possible drizzle over foods.


  • If there is no significant improvement within 2 months, increase the dosage of omega-3 fatty acids. If things still do not improve or seem to plateau after a couple months, Dr. Nemechek will add bioelectric Vagus Nerve stimulation with good results.

  • To gain better control of SIBO in older children Dr. Nemechek  often treat with a 10-day course of Rifaximin (Xifaxan in U.S.).

  • Rifaximin is a non-absorbable antibiotic that is only used for other bacterial overgrowth conditions.

Signs The Nemechek Protocol Is Working

  • At first you may see increased constipation use homeopathy or Milk of Magnesia, or more magnesium) and that is a very good sign that it is working.

  • If you see diarrhea you should do as Dr. Nemechek advises:

    • Start inulin fiber alone for 2-3 weeks in order to let the gut bacteria balance out

    • then slowly increase the dose of fish oil and usually the tolerance is much better.

    • You may also see an increase in behaviors such as stimming, anxiety, aggression, insomnia etc.

    • This is a good sign and indicates that the brain is waking up.

    • This is further explained in the “Why it works!” document.

  • What to look for:

    • signs of increased awareness.

    • A general sense that your child is more ALERT and in tune with the world around him/her.

    • Better eye contact, increased sociability etc.

Important Comments About Avoiding Probiotics

  • The good bacteria eat Inulin.  As they eat and get bigger they naturally secrete an acid that pushes the "bad" bacteria back down into the colon.

  • This is the most natural way to restore normal healthy gut flora.

  • A probiotic keeps everything alive - the Nemechek protocol promotes feeding the GOOD and ignoring the bad.

  • DO NOT give a probiotic while on this protocol that includes any yogurts that promote themselves for their probiotic properties (like Activia for example).

  • The probiotic is keeping both the GOOD and the BAD bacteria alive.

  • To be fair it’s not a bad bacteria - it serves its purpose quite well when it is contained in the colon.

  • In the case of SIBO the bacteria has now spread throughout the small intestine and is decimating the bacteria that typically lives there.

Tips For Treating SIBO With Nemenchek Protocol

  • Keeping SIBO in balance requires diligence and patience and an understanding that there will be flare ups (growths in bad bacteria) that keep allowing it to take the lead again.

  • Many things will cause these flare ups - excessive sugar, carbs, stress, illness

  • Be patient and allow the body time to heal and the brain to resume development.

  • Stay on the protocol and eventually  flare ups will lessen in magnitude. Eventually you have such a numbers advantage over them that they really have not much impact when they flare up.

  • You will see periods of time where symptoms worsen, plateau and disappear. This will cycle until your body gets properly aligned.

Notes From The Book

"The Nemechek Protocol:  For Autism and Developmental Disorders"

Fish are the colon's (large instestine) bacteria...the birds in the small intestine...and probiotics are lizards - completely different and unneeded.


A.  Helpful, normal microglia help us develop normally during childhood.

  • No 2 cases of autism are alike.  Author groups all developmental delays, hyperactivity, tics, and sensory processing disorder, and more into one group with common etiology. 

  • Discussion of mother to child transfer of bacterial makeup:  Miasms. 

B.  Colonic bacteria (fish) are migrating too high into the small intestine (birds). 

C.  Bacterial overgrowth = when colonic bacteria (fish) are living up with the small intestine bacteria (birds).

D.  Bacterial overgrowth causes LPG leakage, which changes cell function to "Primed Microglia."

E.  Primed microglia are no longer helpful, primed microglia are harmful. 

F.  Primed microglia do not perform normal neuron pruning or repair brain injuries. 

  • Awakening period:  Improved neural development:  Catch up 2-3 years for every solid year of treatment (p.65): 

  • Good quote:  "degree of developmental delay underlying each patient's toxic encephalopathy state." (p.68)

  • "The children are not worse, they are finally awake."  (p. 69)

“The cumulative effect of treatment reverses the toxic effect of propionic acid as levels decline, and a reduction in inflammation triggers normal neuronal pruning and the improvement or reversal of eve long-standing developmental delay.”  (p. 34)

Therefore, to achieve:

1. Balance intestinal bacteria. 

  • "Inulin increases the acidity of the small intestine which results in suppressed growth of the colonic bacteria within the small intestine.  When the growth of colonic bacteria is suppressed, propionic acid production is dramatically reduced."  (p. 41).

  • NOW Brand Inulin

  • "Inulin fiber does not kill intestinal bacteria, instead it works like a fertilizer. Inulin fiber nourishes the healthy bacteria that rightfully should be living in the small intestine.  The invading bacteria from the colon are not nourished by the inulin."  (p.41) 

  • Stop probiotics.  Seemingly forever.

  • Stop herbal remedies, fermented foods, digestive aids, and multivitamins. 

2. Shift M1-Microglia towards the Anti-Inflammatory M2-Microglia Phenotype.

  • This rebalance will occur with steps 3 and 4.

3. Balance Omega 6 & Omega 3 Fatty Acids.

  • Cooking with extra virgin olive oil should be enough.  We are giving Robert ˝ teaspoon daily.  When he was given more than ˝ teaspoon, it seemed to cause nausea. (Extra virgin olive oil:  Biblical foundation:  the healing properties of olive oil in The Good Samaritan.)

  • “EVOO contains 70% oleic acid, and oleic acid not only blocks but it also reverses the underlying inflammation coming from excessive omega-6 fatty acid and palmitic acid toxicity.”  (p.59)

  • Check approved olive oils. at

  • Supplement with fish oil or cod liver oil.  Likes the NOW and Nordic Naturals brands.  Wants to be sure they are pure.

  • DHA is the only one capable of penetrating the brain.  There are no substitutes.   DHA dosage recommendations found on p.54. 

  • For cooking and purchasing purposes, canola, coconut, and palm kernel oil okay.  (Easier to remember the good than the many, many bad.)

  • The goal is to reduce metabolic inflammation.

  • Ideal ratio of Omega 6: Omega 3:  1:2.5.  Current in American diet:  20:1.  Yikes!

4. Reduction of brain and systemic inflammation from dietary linoleic, arachidonic, and palmitic acid.

  • Stool pattern p.77:  "If a child has an increased rate of stool production from bacterial overgrowth (i.e., diarrhea) while at the same time has inadequate forward stool propulsion from autonomic nervous system damage (i.e., constipation), they may seem to have a normal stool pattern." 

  • Says there are no yeast die off symptoms on p.87.  (We did see yeast die off symptoms/behaviors during the second week on inulin, akin to antibiotic detox. These lasted a few days and have recurred in short bursts).

5. Induction of Neuroplasticity.

  • This sounds remarkably like AIT:  Vagus nerve and igniting the parasympathetic system.  (p.37)

Potential for Relapse: 

  • Only in patients with prior autism (p.97) 

  • Known triggers:  antibiotics, abdominal surgery, vaccines, antacids, intestinal infection, food poisoning, brain injury, probiotics, and alcohol.  Also, going off of the Nemechek Protocol. 

Key Points

  • Autism is associated with an imbalance of intestinal bacteria and brain inflammation.

  • In normal brain development, neurons must be trimmed or there will be a developmental delay.  This is called pruning.

  • The common cause of altered neuron pruning is impaired function of microglia.

  • In addition to neuron pruning, microglia also repair brain injuries caused by physical, emotional or inflammatory trauma.

  • Bacterial Overgrowth is when colonic bacteria migrate into the small intestine

    • This can create inflammation and send signals through the autonomic nervous system that disrupts  brain function and causes other problems.

    • Also causes fragments of cell membranes to leak into blood and flow into brain to alter function of microglia. 

    • Altered microglia are referred to as “Primed”

Overgrowth  -  LPL  Leakage - Primed Microglia

  • Primed microglia do not prune neurons or repair damage to brain, but rather cause harm.

  • An overgrowth of colonic bacteria also produce propionic acid, which acts as a sedative for the brain and can cause a child to slip into autism.

  • An overproduction can be caused by surgery, antibiotics, etc.


The Nemechek Protocol

Step 1 – Rebalance of intestinal tract

  • Inulin,  1/8-/1/4 teaspoon 1-2 times a day for child 10 years and younger

  • Feeds intestinal bacteria but not colonic bacteria to reverse overgrowth and rebalance gut

Step 2 – Shifting M1 Microglia to anti-inflammatory M2 Phenotype

  • Increase Omega 3 fatty acids with fish oil (DHA & EPA)

  • Helps repair brain

Step 3 – Reduction of Omega 6 fatty acid from diet

  • Cut out the following oils as much as possible:  soybean, sunflower, corn, safflower, cottonseed, grapeseed, peanut, margarine and shortening.

  •  The following oils are acceptable in limited amounts:  Canola, coconut, palm kernel.

  • A healthy ratio of Omega 6 to Omega 3 oils should be roughly 1-2.5 Omega 6  to 1 Omega 3.  This was normal for our ancestors.  But in our diet today the normal consumption ratio is twenty to one Omega 6 to Omega 3.

Step 4 – Prevention of brain and systemic inflammation from excessive dietary linoleic, arachidonic and palmitic acids

  • Difficult to completely avoid

  • Use Extra Virgin Olive Oil (EVOO), sourced from California for quality assurance, for cooking

  • For children 5-10 years, ˝ teaspoon EVOO per day

  • 11-18 years, 1 tspn

  • 19 and older, 2 tspns

Step 5 – Induction of Neuroplasticity

  • Transcutaneous vagus nerve stimulation (tVNS)

  • Most of his patients don’t need this

Awakening Period:

Nemechek says it is normal for patients to go through an awakening period while on the protocol.

  • The initial decline of the toxic effects of propionic acid on the brain can show the true extent of brain dysfunction.

  • May result in immature behavior, angry outbursts, anxiety, hitting, etc.

  • Constipation  and/or diarrhea while the gut gets sorted out.

  • Constipation  and/or diarrhea while the gut gets sorted out.


  • Child may revert to very young behavior (when damage first occurred).

  • May recover 2-3 months of age for every month on the Nemecheck protocol.

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