When families consider starting the Nemechek Protocol, one of the most common fears Dr. Patrick Nemechek hears is that the beginning will be “sheer chaos.” In this video, he addresses that worry directly—based on his clinical experience—by outlining a set of early physiological and behavioral patterns he commonly sees, and why the most intense period (when it happens) is usually temporary.
He also emphasizes that not every child has the same first-stage response. Some show a rapid shift in alertness and awareness, while others may not show that particular pattern at all—yet can still make progress over time.
Dr. Nemechek’s framework: gut bacterial overgrowth and “psychogenic” chemicals
In the framework discussed in the video, Dr. Nemechek describes a premise behind the protocol: bacterial overgrowths in which bacteria associated with the colon are present in the small intestine (which he illustrates as “fish living up with the birds”). In his clinical interpretation, and as he notes, there is “growing evidence” in autism that certain bacteria can produce what he calls psychogenic chemicals.
One specific example he mentions is propionic acid. He adds that he would not be surprised if, in future years, additional chemicals are identified—though in this video he does not list them or make a definitive claim about what all such chemicals are. In his explanation, these chemicals can alter a child’s cognition and awareness. As the intestinal tract becomes more balanced, he describes a reduction in these chemicals and a lifting of what he portrays as a suppressive effect.
The early “Awakening”: what some parents notice
Dr. Nemechek explains that when the protocol reduces these chemicals, it can be “as if you take your child off a potent sedative.” He calls this early stage the “Awakening.”
In his description, the Awakening can include many positive changes, such as:
- More alertness
- Better eye contact
- Improved responsiveness
- Parents reporting the child seems more “present” and aware of what is happening in the room
- Tracking people “for the first time ever” (as some parents describe)
- Sometimes early speech changes
- Sometimes more affection that wasn’t present before
He frames this stage as generally very positive, and he encourages families not to automatically interpret early intensity as a sign that things are going wrong.
When “good” changes come with harder behaviors
Dr. Nemechek notes that a subset of children—because of underlying neurological imbalances, developmental delay, and (as he mentions) injuries—may show the positive “Awakening” features while also having some more challenging short-term changes.
Examples he gives include:
- Insomnia
- Increased agitation
- More aggressive behaviors (for example, pinching)
Importantly, he characterizes this pattern as still including “the good stuff with it.” In other words, the challenging behaviors can appear alongside increased awareness and engagement, rather than replacing them.
Is it always chaos? Dr. Nemechek’s timing expectations
In this video, Dr. Nemechek states that the idea that starting is inevitably chaotic is “not always true,” and in his experience is “often the exception” rather than the rule.
For those who do experience heightened negative features early on, he describes a typical timeframe: if dosing is within the ranges “we discuss” (he references prior dosing discussions rather than detailing them here), the heightened effects usually begin to come down within a few weeks to perhaps two months. He adds that in an older child—such as a teen—this may take longer.
He also describes a common parent experience during this period: the first weeks can feel “a little crazy,” but then families observe improvement and feel they can manage it. His practical message is that families “just got to get through that,” and he encourages not hesitating to use the protocol due to fear of early turbulence.
What if there’s no “Awakening”?
Dr. Nemechek also cautions families not to assume the protocol is failing if the classic Awakening does not occur. He describes that some children may have bacterial overgrowth yet do not make propionic acid (in his wording). In that situation, he says you may not see an Awakening.
He further notes that these can be children who already have good eye contact, awareness, and comprehension—so the contrast may be smaller. In his guidance, the absence of an Awakening does not automatically mean “it didn’t work.” Instead, he recommends waiting a couple of months to assess gains.
The “modified” start some parents try
Dr. Nemechek mentions that some parents use what they call a “modified” Nemechek Protocol. As he describes it, they give fish oil and olive oil first for a month or two, then add the inulin or rifaximin later, with the hope of dampening negative behaviors if they occur.
He states he has never started anybody on the modified protocol and does not see a need for it, but he considers it harmless. His priority, as he puts it, is to get the child started and recovering.
Educational medical disclaimer
Disclaimer: This article summarizes statements made by Dr. Patrick Nemechek in the referenced video and is for educational purposes only. It is not medical advice and is not a substitute for individualized care from a licensed clinician who can evaluate a specific child’s needs.
