CIRS Protocol - Biotoxin Flow Chart

What Is Chronic Inflammatory Response Syndrome?

Table of Contents

Chronic Inflammatory Response Syndrome, or CIRS, occurs when a genetically predisposed person encounters a biotoxin that they are unable to eliminate.

Normally, when the body encounters a toxin, our bodies launch an immune reaction that identifies and eliminates the toxin by creating specialized response units called antibodies. For people with CIRS, the innate immune system will recognize the presence of a biotoxin but the adaptive immune system will fail to create the antibodies needed to remove the biotoxin. The inflammation created by the innate immune response will recycle within the body and cause many downstream symptoms in multiple systems.

Unlike other immunity disorders that are characterized by an inappropriate adaptive immune response, CIRS cannot be identified by traditional autoimmune blood markers like anti-nuclear antibodies or rheumatoid factor. Since people suffering from CIRS have a wide variety of symptoms, they are often misdiagnosed or left untreated.

Biotoxin Flow Chart



Chronic Inflammatory Response Syndrome is sometimes called “mold illness” because 80% of CIRS cases are caused by chronic exposure to a water-damaged building. However, several biotoxins can cause CIRS, including: parasites, algae, Lyme disease, some vaccines, and bacteria. A person’s reaction to a specific biotoxin is indicated by their genetic haplotype and intensity of exposure.

Before CIRS Can Be Treated


Who Might Have CIRS?

Dr. Ritchie Shoemaker, the family care physician who first identified and studied CIRS, found that over 20% of people have genetic haplotypes that indicate susceptibility to CIRS.  According to the Environmental Protection Agency, 50% of buildings in the United States are water damaged. That means that 40 million people in the United States are likely living with CIRS.

If you have been pursuing root cause healing for some time and you are still unwell, unable to lose weight, or require extensive interventions to feel better, then you may want to see if you fit into the diagnostic criteria that indicate more bloodwork is needed.

Who might have CIRS


Diagnostic Criteria

Unlike other chronic illnesses, Chronic Inflammatory Response Syndrome has clear diagnostic criteria, The first two criteria can be completed by the patient before pursuing guidance from a provider.


Criterion One – Symptoms

Having some of the symptoms indicative of CIRS does not necessarily mean you have CIRS. The symptoms are grouped into 13 different clusters based on the different effects of the biotoxin pathway. People who have symptoms in 8 of the 13 should consider completing the next criteria. You only need ONE symptom in a cluster for it to be considered a positive cluster and counted.

What does CIRS look like - Symptoms


Criterion Two – Visual Contrast Sensitivity Test

The Visual Contrast Sensitivity, or VCS, test can be completed for free at This test determines the ability to distinguish between blurred lines. Over time, the white blood cells created by the innate immune system’s response to the biotoxin restrict blood flow in capillaries. The capillaries in the optic nerve are impacted by the reduced blood flow and cause CIRS patients to lose sensitivity to contrast. About 7% of CIRS patients will pass the VCS test, but those that have 8/13 symptom clusters and fail the VCS are over 93% likely to have genetic haplotypes and blood markers indicative of a CIRS diagnosis.

CIRS - Visual Contrast Sensitivity Test


Criterion Three – Blood Work

People that have at least 8 of the 13 symptom clusters and fail the VCS test should work with a provider to complete CIRS-specific blood work. Typically, this blood work tests for the genetic predisposition to CIRS. These haplotypes can indicate which biotoxins will trigger CIRS in a patient.

CIRS blood work may also include markers for the downstream effects of the innate immune system response to the biotoxin. There are four main markers for CIRS: high TGF B-1, C3a and C4a, and MMP9 and low MSH. Additional blood markers may be taken to help the provider better understand the downstream impact of the inflammation. By the end of the protocol, all of these blood markers should be addressed and corrected.

CIRS Bloodwork

Mini CIRS Bloodwork


Criterion Four – Improvement With Treatment

The last criterion is an improvement with treatment. Once the patient completes the foundational steps of the protocol, a CIRS provider will prescribe a medication that has a specific charge and receptor site size that allows it to bind to and remove biotoxins from the body. Working with a CIRS-specific provider is important to achieve root cause healing as this prescription-only binder is necessary to treat CIRS. Traditional detox protocols, including clay and charcoal, may help the patient feel better and manage symptoms but will not cure them. CIRS patients taking the appropriate binder should experience immediate alleviation of symptoms and be able to pass the VCS test after 4 weeks of treatment.



There are four phases to the clinically proven CIRS protocol:

  1. Foundation
  2. Toxic load reduction
  3. Metabolism repair
  4. Repair & Restoration

Each phase must be completed before moving to the next. The final step is a nasal spray that repairs the neural inflammation and restores gene function to normal.

CIRS protocol phases



This phase of the protocol focuses on eliminating the toxic environment, lipid replacement therapy, and limbic retraining. Eliminating the toxic environment is said more easily than it is done. For some, this may mean total remediation of their home, and for others a protocol to treat Lyme disease.  The CIRS provider will guide their patient through the process depending on the suspected biotoxin and potential exposure. The binder used to eliminate the biotoxin may also strip cells of their fatty cell walls. Establishing a healthy omega 3:6 ratio will help people with CIRS better tolerate the treatment protocol.


Limbic Retraining

Did you ever learn about Pavlov’s dogs? Pavlov was a scientist that studied conditioned responses by ringing a bell every time he fed his dogs. Over time, the dogs would salivate at the sound of the bell even when food was not present.

Our brains create neural pathways in response to our experiences, but sometimes inappropriate neural pathways are created mistakenly. For example, have you ever had the stomach flu after eating a specific food, and after that experience, smelling that food made you feel nauseous? Even if that food didn’t cause your illness, your body now associates that smell with being ill.

For people suffering from chronic illness who frequently feel poorly, inappropriate neural pathways are created at a much higher rate. If a bell rang every time you experienced a flare in your symptoms, eventually ringing a bell could become the trigger that causes your body to flare. People may find that they start experiencing histamine reactions to certain foods, scents, or chemicals that were never an issue for them before.

Limbic retraining is the process of re-wiring those neural pathways, so the body does not continue reacting to conditioned triggers. There are many different options for limbic retraining, but the best option for you will be the one you can adhere to.

CIRS Protocol - Foundation Phase


Toxic Load Reduction

The next phase in the protocol is reducing toxic load. At this point, a binder will be prescribed by a CIRS provider. After 4 weeks of treatment, if the patient is able to pass the VCS test, the provider can move on to the next step of the protocol – treating MARCoNS.

Multiple Antibiotic Resistant Coagulase Negative Staphylococci, or MARCoNS, is an antibiotic-resistant staph infection that resides in the nose. People with CIRS are particularly susceptible to MARCoNS and this must be treated and eliminated before moving on to the next step.

Low MSH is one of the hallmark blood markers of CIRS. Melanocyte stimulating hormone, or MSH, has many roles within the body, one of which is regulating tight junctions in the gut. Many people with CIRS experience gastrointestinal issues that are not resolved by traditional GI protocols prior to removing the biotoxin. However, once this has been eliminated, achieving better gut health will help people with CIRS better utilize the supplements used in the following phases of the protocol.

CIRS protocol - Toxic load reduction phase


Metabolism Repair

All of the remaining steps in the protocol are dependent upon the blood markers indicated. The CIRS provider will provide support for detoxing, bringing sex hormones to optimum levels, and balancing electrolytes.

People who have CIRS may have an impaired ability to eliminate other toxins, working with a CIRS provider, they can recommend additional supplements and therapies to support detoxification. Low MSH can reduce androgen production which may require supplementation to bring back to optimal levels. Another side effect of low MSH is decreased production of anti-diuretic hormone production. This hormone helps regulate kidney function and causes an imbalance of electrolytes. As each of these blood markers shows improvement, the CIRS patient can move on to the next step of the protocol.

CIRS protocol - Metabolism Repair phase


Repair & Restoration

The final phase of the protocol is to repair and restore the main blood markers of CIRS: MMP9, TGF, C3a and C4a, and MSH.  Once each of these blood markers is back within normal range, and the patient feels normal again, they are cured of CIRS and should be free of all the downstream symptoms.

CIRS protocol - Repair and restoration phase



Following completion of treatment, patients should continue to work with their provider to manage any unexpected exposure.


The Good News

Chronic Inflammatory Response Syndrome is a diagnosis that provides hope! CIRS symptoms are completely curable and reversible by following the clinically proven protocol. For many people who have suffered from long-term chronic illness, a CIRS diagnosis is a hope for root cause healing they never thought they could have.  

If you eat mostly meat-based or have tried other healing diets but still do not feel 100%, you may be struggling with Chronic Inflammatory Response Syndrome.


Getting Support

You can work more closely with the Nutrition with Judy nutritionist team prior to reaching starting your CIRS protocol in order to set yourself up for optimal healing. Please see our guides for more information on healing and the next steps for people who may have Chronic Inflammatory Response Syndrome.

If you are interested in group support, you can join Jacie Gregory and Barbara Williams’ Carnivore + CIRS group support, here.

This short documentary provides a good glimpse into CIRS. Know that you can heal. The goal is always getting to root-cause healing.


DISCLAIMER: The content is for educational purposes only. While I am board-certified in holistic nutrition and a nutritional therapy practitioner, I am not providing medical advice. Whenever you start a new diet or protocol, always first consult with your trusted practitioner.

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