Article

The Ultimate CIRS Treatment Guide for 2025

November 5, 2025

Medical Disclaimer: This information is for educational purposes only and should not be used as a substitute for professional medical advice, diagnosis, or treatment. Always consult with a qualified healthcare provider familiar with CIRS for personalized medical guidance.

Introduction to CIRS Treatment

Let me guess—you've been to doctor after doctor, each one looking at you like you're making it up. The crushing fatigue that makes you cancel plans. The brain fog so thick you forget simple words. Body pain that moves around like it has a mind of its own.

Sound familiar?

If you've spent time in a water-damaged building (and nearly 50% of us have), you might be dealing with Chronic Inflammatory Response Syndrome (CIRS). It's real, it's treatable, and no—you're not crazy. This complex illness gets misdiagnosed as everything from fibromyalgia to depression because most doctors simply don't know to look for it.

It's a staggering problem. An estimated 25% of the population has a genetic susceptibility to biotoxin illness, and with studies showing that nearly 50% of U.S. homes have evidence of dampness or mold, the risk of exposure is widespread. The intersection of these factors creates what Dr. Craig Tanio calls "an enormous public health challenge"—potentially affecting millions who remain undiagnosed because most physicians don't consider CIRS in their differential diagnosis. Both the CDC and WHO have documented the association between dampness and mold in buildings and various health problems.

"Biotoxin-related illnesses are often misdiagnosed and undertreated, leading to prolonged suffering and disability for countless individuals," notes Dr. Keith Berndtson, a leading physician in complex chronic illnesses. "The key is recognizing the pattern of multi-symptom, multi-system illness that defines CIRS."

Here's what's actually happening: This isn't some simple allergy (not just sneezing and itchy eyes). For about 1 in 4 people, your immune system literally can't recognize and remove biotoxins. Think of it like having a security system that can't see the intruder—so the alarm just keeps blaring. Forever.

But here's the hope you've been searching for: There's a proven, peer-reviewed treatment that actually works. The Shoemaker Protocol has helped thousands reclaim their lives through a systematic, 12-step approach. No quick fixes, no miracle supplements—just real science that addresses the root cause.

This guide will walk you through every single step, from getting properly diagnosed (finally!) to the moment you realize you feel like yourself again.

What is the Shoemaker Protocol?

Think of the Shoemaker Protocol as your roadmap out of CIRS. Developed by Dr. Ritchie Shoemaker through 30+ years of research (and thousands of recovered patients), it's a systematic, 12-step approach that actually makes sense.

Instead of throwing random treatments at symptoms, it works step-by-step to:

Get you out of the toxic environment
Clear biotoxins from your body
Fix the hormonal chaos
Restore your immune system's ability to self-regulate

The best part? When followed correctly, published research shows success rates over 90%. Those aren't marketing numbers—that's peer-reviewed science.

What is CIRS? A Simple Explanation
The 12 Steps of The Shoemaker Protocol
How MoldCo Delivers Expert CIRS Care
CIRS Treatment Timeline & What to Expect
Finding a Qualified CIRS Specialist
Key Treatment Options & Therapies
What Does Recovery from CIRS Look Like?
Key Takeaways
Further Reading & Patient Resources

What is CIRS?

Chronic Inflammatory Response Syndrome (CIRS) is a multi-system, multi-symptom illness caused by exposure to biotoxins in genetically susceptible individuals. These biotoxins—toxic substances produced by living organisms—can come from water-damaged buildings (mold and bacteria), tick-borne illnesses, harmful algal blooms, and other sources.

The Biotoxin Pathway

When biotoxins enter the body, they trigger a complex cascade of inflammatory responses. In most people, the immune system identifies these biotoxins, tags them, and the liver removes them from the body. However, approximately 24% of the population lacks the necessary immune response genes (specific HLA-DR genotypes) to form antibodies against these biotoxins.

"Certain HLA genotypes, particularly HLA-DR and HLA-DQ, are associated with an increased risk of developing biotoxin-related illnesses," notes Dr. Ritchie Shoemaker, the pioneering physician who developed the Shoemaker Protocol through 30 years of research. "These genotypes affect the body's ability to recognize and eliminate biotoxins effectively."

According to published research by Shoemaker and colleagues, VIP deficiency occurs in 98% of CIRS patients compared to less than 10% of healthy controls, demonstrating the profound impact biotoxins have on regulatory neuropeptides.

Common CIRS Symptoms

Here's where it gets tricky—CIRS doesn't just mess with one thing. It's like a cascade effect throughout your entire body:

Neurological: Chronic fatigue, brain fog, memory issues, difficulty concentrating, headaches, light sensitivity

Respiratory: Shortness of breath, chronic cough, sinus problems

Musculoskeletal: Joint pain, muscle cramps, morning stiffness

Gastrointestinal: Abdominal pain, diarrhea

Other: Temperature dysregulation, excessive thirst, static shocks, mood swings and anxiety

The complexity and variety of symptoms often lead to misdiagnosis or dismissal by healthcare providers unfamiliar with biotoxin illness. Understanding why mold affects people differently is crucial for proper diagnosis.

The Shoemaker Protocol: A 12-Step Pyramid to Recovery

The Shoemaker Protocol is a systematic, 12-step treatment approach developed by Dr. Ritchie Shoemaker through decades of research and clinical experience. It is the only peer-reviewed, evidence-based method for treating CIRS. The protocol must be followed in sequence, as each step builds upon the last to systematically cool down inflammation and restore normal function.

"The treatment protocol is simple to understand, yet strict adherence is required in the treatment sequence," states Dr. Shoemaker in his foundational research. "Variations have been attempted and substitutions have been tried... it is critically important to follow the pathway to health in the order it is prescribed."

Why Strict Protocol Adherence Matters: The Shoemaker Protocol is the only peer-reviewed protocol for CIRS treatment, developed through decades of clinical research and validated through published studies. A 2024 systematic review published in the Annals of Medicine and Surgery analyzed all available CIRS treatments and concluded: "The only treatment with documented clinical efficacy was the Shoemaker Protocol, which was described in 11 of the 13 articles. This treatment protocol exhibits superior outcomes compared with the treatment protocols for ME/CFS."

Each step builds on the biochemical changes achieved in the previous steps. Skipping steps or adding unproven treatments can disrupt this carefully orchestrated sequence. Be wary of practitioners who modify the protocol or promise shortcuts—these variations lack scientific validation and may compromise your recovery. The protocol must be followed in order, without skipping steps or adding extra interventions not supported by evidence.

The protocol is often visualized as a pyramid. Everyone starts at the bottom, and as you climb, each step resolves a specific abnormality, leaving fewer and fewer people needing the subsequent steps.

The 12 Steps of the Shoemaker Protocol:

Remove from exposure and test your environment
Cholestyramine (CSM) or Welchol binder therapy
Eradicate MARCoNS (nasal staph colonization)
Eliminate gluten if antigliadin antibodies present
Correct androgen levels
Correct ADH/osmolality dysregulation
Reduce MMP-9 with low-amylose diet
Normalize VEGF levels
Address elevated C3a
Re-evaluate C4a
Lower TGF-β1
VIP nasal spray therapy

Step 1: Remove from Exposure & Test Your Environment

The absolute, non-negotiable foundation of CIRS treatment is removing the patient from biotoxin exposure. Treatment cannot succeed if you are still being exposed to a water-damaged building (WDB). It's like trying to bail out a boat with a hole in it.

The statistics on building dampness are sobering. According to research compiled by Berkeley Lab, an average of 47% of U.S. homes have dampness or mold. A U.S. EPA survey of 100 office buildings found that 85% had past water damage and 45% had current leaks. As the EPA emphasizes, the key to mold control is moisture control.

Actionable Steps:

Test Your Environment: Use a validated test like the Environmental Relative Moldiness Index (ERMI) or HERTSMI-2 to quantify the mold burden in your home. A HERTSMI-2 score below 11 is considered safe for CIRS patients. Learn more about professional mold testing options.
Remediate or Relocate: If testing reveals an unsafe environment, professional mold remediation or relocation is essential. Remediation must follow strict protocols, like the IICRC S520 standard. Understanding the difference between mold removal and remediation is crucial.
Assess All Environments: Test your workplace, school, and any other building where you spend significant time. Hidden mold sources can perpetuate symptoms even after home remediation.

Important Insurance Considerations: Most homeowners insurance policies have limited mold coverage, typically ranging from $1,000-$10,000 per occurrence. According to Bankrate's 2024 insurance analysis, mold damage is only covered when it results from a "covered peril" such as burst pipes or storm damage. The Insurance Information Institute notes that after the toxic mold crisis of the early 2000s, insurers specifically excluded or limited mold coverage. Professional remediation costs average $15,000-$30,000 and often exceed insurance limits, so be prepared for significant out-of-pocket expenses. Some states allow purchase of additional mold coverage endorsements for $25-$100 annually.

"For many people, this is the most critical, yet most difficult step," emphasizes Dr. Bruce Hoffman, a certified Shoemaker Protocol practitioner. "Without removing exposure, treatment cannot succeed."

Unsure if your home is safe? Start with a HERTSMI-2 home test to get definitive answers.

Step 2: Prescription Binder Therapy (Clinician-Directed)

To reduce biotoxin re‑circulation, Shoemaker‑licensed clinicians may prescribe bile‑acid sequestrants such as cholestyramine or colesevelam (Welchol). These medications bind biotoxins in the bile and prevent their reabsorption, allowing safe elimination through the digestive system.

Choice of agent, formulation, and schedule are individualized based on history, tolerance, and labs. According to clinical data published in Dr. Shoemaker's research, patients on binder therapy typically show significant improvements within 30 days, with Visual Contrast Sensitivity (VCS) scores improving in over 92% of compliant patients.

MoldCo providers often prefer Welchol (colesevelam) due to its better tolerability and convenient tablet form, though your provider will determine the most appropriate binder based on your individual needs. Binder use should be supervised by a qualified clinician; patients should review risks and contraindications with their healthcare provider.

"Cholestyramine is like a sponge that soaks up biotoxins and helps remove them from the system," explains Dr. Neil Nathan, a certified Shoemaker Protocol practitioner. "We typically see a 30-50% reduction in symptoms within the first month of therapy, particularly in neurological symptoms like brain fog and fatigue."

Improvements are tracked through regular VCS testing, symptom questionnaires, and monitoring of inflammatory biomarkers like MMP-9 and C4a.

Step 3: Eradicate MARCoNS

MARCoNS (multiple‑antibiotic‑resistant coagulase‑negative Staph) can colonize the nasal passages and perpetuate inflammation by disrupting MSH. According to published clinical data from Dr. Craig Tanio, MSH deficiency is highly correlated with the presence of MARCoNS—less than 1% of patients with normal MSH levels have MARCoNS colonization. These bacteria release hemolysins A and B which cleave MSH, creating a vicious cycle that perpetuates immune dysfunction.

Diagnosis requires a deep nasal culture through a specialized lab. If present, your provider may prescribe a compounded intranasal therapy with antimicrobial and chelating agents to address the colonization and break down the protective biofilm. Your provider will determine the appropriate treatment protocol and duration. Re-testing is required to confirm clearance, as complete eradication is essential before advancing in the protocol.

Step 4: Eliminate Gluten (If Antigliadin Antibodies are Present)

If blood tests show positive antigliadin antibodies (AGA), a strict gluten-free diet is implemented for three months, after which the labs are re-tested. According to Dr. Craig Tanio's clinical review, 33% of adult CIRS patients have elevated antigliadin antibodies. This step addresses a potential source of gut-related inflammation that can perpetuate the CIRS cascade through intestinal permeability. It does not necessarily mean the patient has celiac disease—the antibodies reflect T-regulatory cell dysregulation secondary to low MSH rather than true celiac pathology.

Step 5: Correct Androgens

Low androgen levels are common due to increased aromatase activity secondary to low MSH. According to the VIP therapy trial data, testosterone levels in male CIRS patients averaged 299 ng/dL (normal >415), improving to 512 ng/dL after treatment. Your provider will address hormone imbalances as upstream inflammation resolves, with lab results guiding any targeted interventions. Direct testosterone supplementation is typically avoided in early treatment stages as elevated aromatase can convert it to estradiol.

Step 6: Correct ADH/Osmolality

Dysregulation of antidiuretic hormone (ADH) and serum osmolality occurs in 80% of CIRS patients, according to Dr. Tanio's clinical data. This dysregulation can drive excessive thirst (polydipsia), frequent urination (polyuria), and static shocks. Your provider will determine if medication is needed to correct this pattern, with close monitoring of electrolytes and serum osmolality to ensure sodium levels remain normal while addressing upstream inflammation.

Step 7: Reduce Elevated MMP-9 with a Low-Amylose Diet

Matrix metalloproteinase-9 (MMP-9) is a key inflammatory marker that reflects cytokine activity and "leaky" junctions—in the gut, lungs, and brain. Normal MMP-9 levels range from 85-332 ng/ml, but CIRS patients often present with levels exceeding 600 ng/ml. According to the VIP therapy trial, patients' MMP-9 levels averaged 628 ng/ml at baseline, normalizing to 290 ng/ml after treatment.

To lower MMP-9, your provider may recommend a low-amylose diet, which eliminates starchy foods like grains, potatoes, and bananas that can contribute to inflammation. Your provider will also discuss appropriate nutritional support strategies to help reduce inflammatory expression.

Step 8: Support Low VEGF (Vascular Endothelial Growth Factor)

Low vascular endothelial growth factor (VEGF) is associated with poor oxygen delivery to tissues, leading to fatigue, muscle cramps, and post-exertional malaise. Normal VEGF ranges from 31-86 pg/ml. Dr. Tanio's clinical review notes that low VEGF creates anaerobic mitochondrial metabolism, resulting in decreased muscle endurance and a low VO2max—CIRS patients often have VO2max levels below 20 (normal >35), comparable to stage IV heart failure patients who typically measure 12-15.

The same dietary strategies used for MMP-9—particularly the low-amylose diet—may also help normalize VEGF levels. If levels remain low after dietary intervention, your provider may recommend carefully structured exercise protocols tailored to your current capabilities.

Step 9: Address Elevated C3a

Persistently elevated C3a, a component of the complement system, can indicate ongoing immune activation, often from difficult-to-detect infections like Lyme disease co-infections. Clinicians use targeted, stepwise anti-inflammatory strategies as indicated while investigating potential underlying causes.

Step 10: Re-evaluate C4a

C4a is a critical inflammatory marker that tracks the severity of the innate immune response in CIRS. Normal C4a levels are 0-2830 ng/ml, but CIRS patients in the VIP therapy trial presented with baseline levels averaging 8346 ng/ml—nearly three times the upper limit. In the past, specific medications were used to lower it, but current practice within the Shoemaker Protocol is to complete the prior steps and re-assess all inflammatory markers. If C4a remains high, it confirms the powerful inflammatory state driven by biotoxin exposure. Notably, C4a levels above 20,000 may require HERTSMI-2 scores below 8 (rather than the standard <11) for safe re-entry into remediated buildings.

Step 11: Lower TGF-β1

Transforming growth factor beta-1 (TGF-β1) is a complex protein that, when elevated in CIRS, can promote autoimmune responses and tissue remodeling (fibrosis). Normal TGF-β1 levels are below 2,380 pg/ml, yet CIRS patients often present with extreme elevations—the VIP therapy trial participants averaged 12,579 pg/ml at baseline, more than five times normal. When levels exceed 10,000 pg/ml, patients can develop interstitial lung disease, pulmonary hypertension, tremor, cognitive issues, joint pain, and hair loss.

Your provider may prescribe specific medications to help lower TGF-β1 when indicated, with careful monitoring of blood pressure and symptoms throughout treatment.

Step 12: VIP Therapy (The Final Step)

Vasoactive intestinal polypeptide (VIP) is a powerful regulatory neuropeptide that is deficient in nearly all CIRS patients. It is the final and most restorative step of the protocol, reserved for patients who meet strict criteria: a safe environment (ERMI <2, HERTSMI-2 <11), a clear VCS test, and no MARCoNS.

An open-label trial published in 2013 by Dr. Ritchie Shoemaker and colleagues demonstrated the remarkable efficacy of VIP therapy. In 20 refractory CIRS patients who had failed all other treatments, 18 months of VIP nasal spray therapy achieved:

100% of patients experienced enhanced quality of life
Symptom reduction from 29.8 to 3.4 (control group averaged 2.9)
C4a levels dropped from 8346 to 3306 ng/ml (normal <2830)
TGF-β1 reduced from 12,579 to 4040 ng/ml (normal <2380)
MMP-9 normalized from 628 to 290 ng/ml (normal <332)
T-regulatory cells increased from 8.9 to 22.5
Pulmonary artery systolic pressure during exercise returned to normal
Testosterone levels in males increased from 299 to 512 (normal >415)
25-OH Vitamin D levels normalized

"VIP replacement therapy has been a game-changer for many of my CIRS patients," says Dr. Shoemaker. The 2013 study he co-authored concludes that VIP therapy safely "restored clinical functioning in a cohort of CIRS-WDB patients with severe illness characterized by profound, refractory abnormalities in innate immune inflammatory responses."

Your provider will determine the appropriate VIP dosing protocol based on your individual response and needs. This final step helps correct the deepest layers of immune and hormonal dysregulation, often resolving lingering symptoms and restoring brain function.

How MoldCo Delivers CIRS Care: A Standardized, Evidence-Based Protocol

Navigating CIRS can be overwhelming. MoldCo simplifies the journey by strictly adhering to the evidence-based Shoemaker Protocol. As a Shoemaker-licensed group led by Dr. Scott McMahon, our trained clinicians deliver this standardized sequence to ensure safe, consistent, and effective care.

"After seeing over 2,000 CIRS patients and completing extensive training under Dr. Shoemaker himself, I've witnessed the transformative power of this protocol when properly implemented," states Dr. Scott McMahon, MoldCo's Medical Director. "Our systematic approach ensures every patient receives the same evidence-based care that has helped thousands recover."

As the only telehealth platform working directly with Dr. Shoemaker to provide the most current protocol updates, MoldCo offers a unique advantage. Our testing is priced 40-60% below standard lab pricing, making comprehensive CIRS evaluation accessible to more patients. The MoldCo Starter Panel, priced at $99, typically costs $150-200 through traditional channels.

The importance of proper CIRS treatment extends beyond individual patients. As Dr. Andrew Heyman, Director of Integrative Medicine at George Washington University and co-author of "The Art and Science of CIRS," emphasizes: "Up to 20% of the US population is vulnerable to biotoxin exposures, leading to chronic fatigue, fibromyalgia, neuroinflammatory disorders, cardiopulmonary problems, gastrointestinal dysfunction, and immune impairment. Every primary care provider and functional practitioner must know how to treat this condition since it is so common."

Our clinical approach includes:

Comprehensive Evaluations: Conducted via secure telehealth with labs ordered through accredited partners including LabCorp and Quest Diagnostics
Environmental Safety Assessment: Using EPA and WHO guidelines, with ERMI/HERTSMI-2 testing through EnviroBiomics, the laboratory recommended by Dr. Shoemaker
Data-Driven Progress Tracking: Regular monitoring of Visual Contrast Sensitivity (VCS), symptom clusters, and inflammatory biomarkers (C4a, TGF-β1, MMP-9, VEGF) to ensure treatment efficacy
Strict Protocol Adherence: Each step is completed in sequence, with advancement only when specific criteria are met

This approach is designed for safety, consistency, and outcomes—and to keep the experience simple for patients navigating a complex illness.

Note: MoldCo provides testing services and connects patients with CIRS-specialized providers who determine appropriate treatment protocols. All medical decisions are made by your healthcare provider based on your individual test results and health history.

Ready to understand your symptoms? Take our eligibility quiz to see if you're a candidate for MoldCo's CIRS program.

CIRS Treatment Timeline & What to Expect

CIRS recovery is a marathon, not a sprint. While individual timelines vary based on the severity of illness, duration of exposure, and genetic factors, the journey follows a predictable path. Understanding the phases of recovery helps you manage expectations and stay motivated.

What to Expect from Your First MoldCo Appointment

Your first step with a MoldCo clinician is a comprehensive evaluation via secure telehealth. This is what it typically involves:

Deep Dive into Your History: Your clinician will review your detailed symptom history, exposure timeline, and previous diagnoses.
Order Foundational Lab Work: Based on your history, your clinician will order the necessary CIRS biomarker tests through our accredited lab partners. This often includes markers like C4a, TGF-β1, and MMP-9 from our Starter Panel.
Environmental Assessment Plan: You will be guided on how to properly test your home using an ERMI or HERTSMI-2 test to confirm or rule out ongoing exposure.
Initial Treatment Plan: You'll leave with a clear plan of action and an understanding of the first steps of the Shoemaker Protocol.

Phase 1: Foundational Steps (Months 1-3)

This initial phase focuses on the first three steps of the protocol pyramid.

Weeks 1-2: Conduct environmental testing (ERMI/HERTSMI-2) and create a plan for remediation or relocation if needed.
Weeks 2-4: Begin clinician-directed binder therapy (Cholestyramine or Welchol) to start removing biotoxins.
Month 2: Test for MARCoNS and begin nasal spray treatment if the culture is positive.
Month 3: Your first follow-up labs are typically drawn to assess progress and adjust treatment.

Expected Improvements:

30-50% reduction in the most acute symptoms (headaches, fatigue, cognitive issues).
Improved energy and mental clarity.
Normalizing Visual Contrast Sensitivity (VCS) scores.
A measurable reduction in key inflammatory markers like MMP-9.

Phase 2: Correcting Systemic Imbalances (Months 3-6)

Address dietary changes (gluten-free if needed, low-amylose diet to lower MMP-9).
Correct hormonal imbalances (androgens, ADH/osmolality).
Continue monitoring progress with regular lab work and VCS testing.

Key Milestones:

MMP-9 and VEGF levels normalize.
ADH/osmolality balance is restored, reducing issues like excessive thirst and static shocks.
Continued and more stable symptom improvement.

Phase 3: Advanced Immune & Inflammatory Correction (Months 6-9)

Treat elevated complement markers (C3a, C4a).
Address stubbornly high TGF-β1 levels.
Prepare for the final step of the protocol by ensuring all prerequisites are met.

Phase 4: Final Recovery with VIP (Months 9-12+)

Patient must meet strict criteria before starting VIP therapy.
VIP nasal spray is typically used for at least one month, with some patients requiring longer courses.
This final step addresses remaining symptoms, helps repair neurological function, and supports long-term recovery.

"By this time, most patients will already have become much better with reduction or resolution of at least 75% of their baseline symptoms," according to Dr. Shoemaker's clinical research.

Important Timeline Considerations

Factors that may extend the timeline:

Continued Exposure: This is the most common reason for treatment failure and resets the entire process.
Severe Illness: Longer or more intense exposures can require a longer recovery period.
Complications: The presence of MARCoNS or certain co-infections can add time to the protocol.
Compliance: Strict adherence to the protocol sequence is crucial for timely success.

Factors that may accelerate recovery:

Early and accurate diagnosis.
Swift and complete removal from the toxic environment.
Excellent compliance with all protocol steps and dietary changes.

Monitoring Your Progress

Regular reassessment is key to ensuring your treatment stays on track.

Monthly: Symptom Cluster Questionnaires and VCS Testing.
Every 3 months (or as directed): Comprehensive lab work to track biomarkers.
As needed: Environmental re-testing if symptoms return or new exposure is suspected.

Advanced Monitoring with GENIE Testing: For patients requiring deeper insights into their treatment progress, the GENIE (Gene Expression: Inflammation Explained) transcriptomics test offers sophisticated monitoring capabilities. This advanced blood test analyzes gene expression patterns specific to CIRS, allowing Shoemaker Protocol practitioners to track your cellular response to treatment at the molecular level. According to published transcriptomics research by Shoemaker and colleagues, GENIE testing has demonstrated dramatic changes in the up- and down-regulation of ribosomal and mitochondrial genes following VIP treatment, providing objective evidence of cellular recovery. Many certified practitioners use GENIE testing to confirm treatment progress and distinguish CIRS from other conditions that may present similarly.

Remember, CIRS recovery is not always a straight line. Some patients experience temporary setbacks or intensification reactions as the body eliminates stored biotoxins. Working closely with an experienced practitioner is essential for navigating these challenges successfully.

Finding CIRS Specialists

Finding a practitioner experienced in CIRS treatment is crucial for successful recovery. Not all healthcare providers are familiar with biotoxin illness, and working with someone trained in the Shoemaker Protocol significantly improves outcomes.

What to Look For

Essential Qualifications:

Shoemaker Protocol certification or training
Experience with biotoxin illness and environmental medicine
Understanding of required laboratory testing
Willingness to follow the systematic protocol

Red flags to avoid:

Practitioners who skip steps or modify the protocol
Those unfamiliar with HERTSMI-2/ERMI testing
Providers who don't order appropriate biomarker labs
Anyone promising quick fixes or alternative protocols without evidence

Types of Practitioners

Functional Medicine Doctors: Often have the most comprehensive training in complex chronic illness

Environmental Medicine Specialists: Focus specifically on environmental triggers

Integrative Medicine Practitioners: Combine conventional and evidence-based complementary approaches

Questions to Ask Potential Providers

How many CIRS patients have you treated?
Do you follow the Shoemaker Protocol?
What labs do you typically order for diagnosis?
How do you assess environmental exposure?
What is your typical treatment timeline?

CIRS Treatment Options & Supportive Therapies

While the Shoemaker Protocol provides the sequential framework, it's helpful to understand the specific tools your clinician may use at each step.

Prescription Medications

These are foundational to the protocol and are used to address specific abnormalities uncovered in your lab work.

Biotoxin Binders:

Welchol (Colesevelam): A second-generation bile acid sequestrant that MoldCo providers often recommend as the primary biotoxin binder. Its tablet form and better tolerability profile make it easier for many patients to maintain compliance throughout treatment. Your provider will determine the appropriate dosing schedule based on your individual needs.
Cholestyramine (CSM): The original gold-standard binder that has been used successfully in the Shoemaker Protocol for decades. While highly effective, some patients find the powder form challenging. Your provider will help determine which binder is most appropriate for your situation.

Other Key Medications:

Nasal Treatments: Your provider may prescribe compounded nasal sprays to address MARCoNS colonization when present.
Hormone Support: Medications may be prescribed to help correct ADH/osmolality imbalances and other hormonal disruptions.
Inflammatory Control: Your provider may recommend specific medications to help lower elevated inflammatory markers like TGF-β1.
VIP Therapy: The final step of the protocol, carefully supervised by your provider to help restore regulatory function.

Supportive Therapies & Diet

Lifestyle and dietary changes are crucial for supporting the protocol and reducing overall inflammation.

Dietary Interventions:

Low-Amylose Diet: A key intervention for lowering elevated MMP-9. This involves avoiding starchy foods like grains, sugar, potatoes, and bananas.
Gluten-Free Diet: Implemented for a trial period if antigliadin antibodies are positive.
High-Dose Omega-3s: Specific ratios of EPA and DHA are used to help lower MMP-9.

Supplementation:

While the Shoemaker Protocol does not rely on a large number of supplements, some may be used judiciously by your clinician to address specific deficiencies or support detoxification pathways. All supplementation should be clinician-guided.

Environmental Modifications

Creating a safe "sanctuary" environment is paramount for recovery.

At Home:

Professional Mold Remediation: Must be done according to IICRC S520 standards if your home is the source.
High-Quality Air Filtration: Using HEPA air filters can significantly reduce airborne particulates.
Dehumidification: Keeping indoor humidity below 50% is crucial to prevent new mold growth.

Lifestyle Adjustments:

Vigilance: Become skilled at recognizing and avoiding potentially water-damaged buildings.
Awareness: Understand that as a genetically susceptible individual, you will always need to be mindful of your environment.

Recovery from CIRS: What to Expect

Recovery from CIRS is possible, but it requires patience, persistence, and a realistic outlook. Understanding the typical recovery arc helps you stay the course during challenging moments.

Early Recovery (First 3 Months)

Let's be honest—the beginning can feel like a rollercoaster. Some days you'll feel amazing, others you might wonder if it's working. This is totally normal, and we've seen it thousands of times.

Common Experiences:

Initial Improvement: Many patients feel a noticeable lift in brain fog and fatigue once they are out of exposure and start binders.
Intensification Reactions vs. Herxheimer: What patients often call "Herxheimer reactions" are actually intensification reactions, particularly common in Lyme patients starting cholestyramine. According to Dr. Shoemaker, this intensification occurs at dose 6-10 (day 2-3) and differs from true Herxheimer reactions.
The mechanism involves stored biotoxins being pulled from tissues, entering the bile, then the gut, where they can trigger inflammatory responses. Those at highest risk include the elderly, frail patients, and those who've been ill for over 10 years.
Managing Intensification: To minimize these reactions, practitioners may recommend starting slowly with cholestyramine, implementing a low-amylose diet first to reduce MMP-9 levels, and in some cases, using pretreatment protocols to block excessive inflammatory responses.
Fluctuating Symptoms: Good days and bad days are normal. The goal is a steady increase in the number of good days over time.

Managing Expectations:

Recovery is a process of "two steps forward, one step back."
Some symptoms, like fatigue and body pain, may improve before more complex neurological symptoms do.
Consistency is everything. Sticking to the protocol even when you feel better is key to preventing relapse.

Mid-Recovery (3-9 Months)

This is where the hard work really starts to pay off with more consistent and sustained improvements.

Positive Changes:

More sustained energy and stamina.
Clearer thinking, better memory, and quicker word recall.
Noticeable reduction in body pain, joint aches, and headaches.
Improved mood, motivation, and a feeling of "coming back to life."

Potential Challenges:

Discovering Hidden Exposures: A sudden return of symptoms might mean you've been re-exposed at work, in your car, or another location.
Treatment Fatigue: Sticking with the diet and medication schedule can be challenging. This is where leaning on your practitioner and support systems is crucial.

Long-Term Recovery & Life After CIRS (9+ Months)

By the time patients reach the final steps of the protocol, they are often feeling dramatically better. The goal now is to achieve full recovery and maintain it.

Life After CIRS:

A Return to Normalcy: Resuming work, hobbies, and social activities that were once impossible.
Increased Resilience: Many patients who complete the protocol find they can tolerate minor, brief exposures without relapsing.
Ongoing Vigilance: You will have a new "superpower"—the ability to quickly detect moldy environments. Protecting yourself from future water-damaged buildings is a lifelong skill.

Understanding Re-exposure and What "Cure" Really Means:

It's crucial to understand that successful CIRS treatment doesn't confer complete immunity to future biotoxin exposure. Recovery means your inflammatory cascade has been reset and your body is functioning normally again, but your genetic susceptibility remains.

According to Dr. Shoemaker's research, VCS deficits return within 3-5 days of re-exposure to a water-damaged building in previously treated patients. This rapid return of symptoms underscores the importance of maintaining a biotoxin-free environment.

For safe re-entry after remediation, environments should test below specific thresholds: a HERTSMI-2 score below 10 provides approximately 98% safety for re-entry for most CIRS patients. Regular monitoring of your environment remains essential, as even successfully treated patients will experience rapid symptom return if re-exposed to biotoxins.

"While the road to recovery from CIRS can be long and complex, many patients are able to achieve significant improvement in their symptoms and quality of life with the right treatment approach," emphasizes research in the field.

Key Takeaways

CIRS is a real, diagnosable illness caused by an immune system that can't remove biotoxins. A full overview of testing can be found in our CIRS Testing Guide.
An estimated 25% of people are genetically susceptible, and nearly 50% of buildings have water damage.
The Shoemaker Protocol is the only evidence-based, peer-reviewed treatment for CIRS.
Treatment must be sequential. Each of the 12 steps builds on the one before it.
Removing yourself from exposure is the non-negotiable first step. You cannot heal in a toxic environment.
Recovery is a marathon, not a sprint, but with the right protocol and guidance, it is achievable.

Resources & Support

Educational Resources

Official protocol information:

MoldCo is the primary resource for Shoemaker Protocol guidance
Published research papers on biotoxin illness
Practitioner training materials from Dr. Shoemaker and Dr. McMahon

Testing resources:

MoldCo Testing Guide — comprehensive testing options
Home Testing Options

Support Communities

Online support:

CIRS support groups on social media
Patient forums and discussion boards
Virtual support meetings

Local resources:

Environmental illness support groups
Functional medicine communities
Mold-safe housing networks

Continued Learning

Stay informed:

Subscribe to practitioner newsletters
Attend patient education webinars
Read latest research updates
Connect with recovery success stories

Remember, you're not alone in this journey. With proper treatment, support, and persistence, recovery from CIRS is achievable. The key is finding the right practitioner, following the protocol systematically, and maintaining a safe environment.

Frequently Asked Questions

How long does CIRS treatment take? Most patients require 9-12 months to complete the full Shoemaker Protocol, though timelines vary based on severity of illness, duration of exposure, and genetic factors. Approximately 90% of patients who follow the protocol correctly achieve significant improvement.

Can you recover from CIRS completely? Yes, recovery is possible with proper treatment. The 2013 VIP therapy trial showed 100% of participants experienced enhanced quality of life, with symptoms reducing from an average of 29.8 to 3.4. However, genetic susceptibility remains, requiring lifelong environmental vigilance.

What is the success rate of the Shoemaker Protocol? Published research demonstrates success rates exceeding 90% when the protocol is followed correctly. The 2024 systematic review confirmed it as the only treatment with documented clinical efficacy for CIRS.

Take the Next Step on Your Recovery Journey

You've made it this far—don't spend another year wondering what's wrong. If you're dealing with these symptoms or have been exposed to a water-damaged building, it's time to get real answers.

The Shoemaker Protocol has helped thousands of people just like you go from "medical mystery" to "feeling human again." With the right testing, the right provider, and a proven protocol, recovery isn't just possible—it's probable.

1. Get Definitive Answers with Biomarker Testing Don't guess about your health. Our MoldCo Starter Panel tests key CIRS biomarkers including C4a, TGF-beta-1, and MMP-9. This provides the foundational data needed to understand your inflammatory response and guide treatment.

2. Ensure Your Environment is Safe You can't get well in a sick building. Our HERTSMI-2 Home Test uses the same lab methods recommended by Dr. Shoemaker to assess your home's mold burden and determine if it's safe for occupancy.

3. Get Expert Guidance & a Clear Plan Download our free CIRS Recovery Guide for a step-by-step plan covering everything from initial testing to finding the right practitioner. This comprehensive resource includes home inspection checklists, symptom tracking tools, and treatment timelines.

4. Assess Your Symptoms Not sure if your symptoms point to CIRS? Our free Signs & Symptoms Questionnaire is a validated screening tool that considers your symptoms, exposure history, and risk factors to provide personalized recommendations.

Don't Wait to Get Help

CIRS is a progressive condition—the longer you wait, the more challenging recovery can become. Whether you're just beginning to suspect biotoxin illness or you're ready to start a proven treatment protocol, we're here to support you.

Take your first step today:

Order Lab Testing - Get objective answers with our comprehensive biomarker panel.
Test Your Home - Ensure your environment supports healing.
Download the Free Guide - Access our complete CIRS recovery roadmap.
Take the Symptom Quiz - Assess your risk factors in under 5 minutes.

Medical Disclaimer

This comprehensive guide is for educational and informational purposes only and does not constitute medical advice, diagnosis, or treatment recommendations. The Shoemaker Protocol is a medical treatment that requires supervision by a qualified healthcare provider trained in biotoxin illness.

Individual results may vary significantly based on genetic factors, severity of illness, duration of exposure, and treatment compliance. The statistics and outcomes cited are from published research and may not reflect your individual experience.

Always consult with a Shoemaker-certified practitioner or qualified healthcare provider familiar with CIRS before beginning any treatment protocol. Never discontinue prescribed medications or alter your treatment plan without medical supervision.

The links to products and services are provided for informational purposes. MoldCo and its affiliates make no representations about the suitability of any treatment for your specific condition.