The CIRS Protocol: A 12-Step Treatment Plan
TL;DR
The most widely recognised treatment for CIRS is a 12-step protocol developed by Dr. Ritchie Shoemaker. It follows a sequential order, with each step building on the last. The steps move from removing yourself from biotoxin exposure, through binding and clearing toxins, to correcting the inflammatory markers that CIRS disrupts. It's not quick, it's not simple, and it needs to be done with a practitioner who understands it. This post breaks down each step in plain language, along with where I currently am in the process.
Once you know what CIRS is, the next question is obvious. How do you actually treat it?
That's where the Shoemaker Protocol comes in. Developed by Dr. Ritchie Shoemaker over 30+ years of clinical research with more than 14,000 patients, it's the only peer-reviewed, published protocol designed to treat CIRS at the root cause.
The protocol has 12 steps. Each one is sequential. You can't skip ahead, and you can't cherry-pick the ones that sound easiest. Each step creates the conditions for the next one to work, and doing them out of order is one of the most common mistakes people make.
I'm currently in the early stages myself - still figuring out Step 1 and actively on Step 2 - so this post is part explainer, part real-time documentation. If you're not sure what CIRS is or how it's diagnosed, I'd recommend reading my post "What is CIRS? A Simple Explanation" first.
Before you start: the reality of following this protocol
Before I get into the 12 steps, I want to set some expectations. When I first saw this protocol laid out, I felt overwhelmed - lab markers I'd never heard of, medications I couldn't pronounce, twelve steps that all seemed equally urgent. So here's what I wish someone had told me upfront.
- You don't need to understand all 12 steps right now. You just need to focus on the one you're on. The rest will make more sense as you get there.
- "Perfect" conditions aren't always feasible straight away. The protocol says remove yourself from exposure first. In practice, that's the hardest step of the whole thing - leases, finances, family. A good practitioner works with you pragmatically rather than waiting for perfect conditions.
- Your body may not tolerate standard doses immediately. Many CIRS patients have histamine issues, gut problems and multiple sensitivities. Sometimes a lower dose, built up gradually, is the smarter path.
- Progress is possible even when things aren't textbook. My home tested borderline, yet on a smaller dose of binders I've seen real improvements after a month.
- Don't let perfect be the enemy of progress. The protocol is the goal. The path to get there isn't always a straight line.
The 12 steps
Each step below includes what it involves and, where relevant, where I personally am with it right now.
Step 1Remove yourself from exposure
This is the foundation of the entire protocol. You cannot heal in the environment that made you sick.
In practical terms, this means identifying whether you're living or working in a water-damaged building and removing yourself from it. The way you test this is through an ERMI or HERTSMI-2 test, which measures fungal DNA levels in dust samples from your home or workplace.
On paper, this step sounds simple. In reality, it's by far the hardest. I live in Indonesia, and in tropical climates mold is everywhere - the humidity is constant, building standards are different, and rental leases don't care about your HERTSMI-2 score. In countries where mold illness isn't recognised as a medical condition, there's no legal framework to help you break a lease or demand remediation.
Where I am with this step
My apartment came back with a HERTSMI-2 score of 14. Ideally you want under 10, so it's borderline - not terrible, but it means I'm still dealing with some exposure. I've focused on what I can control: air purifiers in both bedrooms, a dehumidifier in the living area, hydrometers in each room, and daily airflow by opening the balcony door and windows. A separate post on my exact setup is coming.
If moving immediately isn't realistic, don't let that stop you from starting the conversation with a practitioner. There are things you can do to reduce exposure even if you can't eliminate it overnight.
Step 2Biotoxin binders
Once you've removed yourself from exposure (or reduced it as much as possible), the next step is binding the toxins still circulating in your body so they can be eliminated. There are two main binders used in the Shoemaker Protocol.
Cholestyramine (CSM) is the stronger of the two - a prescription bile acid sequestrant with the highest binding affinity for biotoxins and the most clinical evidence behind it. But it comes with more side effects, particularly digestive issues, and needs to be taken on an empty stomach.
Welchol (Colesevelam) has roughly a quarter of the binding capacity, but it's significantly better tolerated, comes in tablet form and can be taken with food. A lot of practitioners now start sensitive patients on Welchol because staying on it consistently matters more than raw potency.
One important note
These are not the same as over-the-counter binders like activated charcoal or bentonite clay, which don't have the correct molecular charge to bind biotoxins effectively. CSM and Welchol are the only binders with published clinical evidence for CIRS.
Treatment runs for a minimum of 30 days, and the VCS test is repeated to measure progress. Side effects like constipation need to be actively managed, because constipation slows toxin removal.
Not everyone can start at the recommended dose. The standard Welchol dose is 6 tablets daily. For many CIRS patients dealing with histamine issues, gut problems and multiple sensitivities, jumping straight to that can make things worse before they get better. A gradual build-up is often smarter.
Preparing for binders. Before I started Welchol, my practitioner had me do a two-week reset diet - just meat, eggs, fish, water and salt - to calm my system down. Painfully boring, but it genuinely helped. He also started me on high-dose Omega 3s, which aligns with the protocol: high-dose fish oil before and during binder treatment can minimise side effects.
Where I am with this step
I started on just 1 Welchol tablet daily, then moved up to 2 (the recommended dose is 6, so I'm still well below it). After over a month, I'm seeing genuine improvements - even in a borderline environment. Brain fog is the symptom that has lifted most noticeably, and after years of struggling to think clearly, that shift alone has been significant.
Step 3Treat MARCoNS
MARCoNS stands for Multiple Antibiotic Resistant Coagulase Negative Staphylococci - an antibiotic-resistant staph bacteria that colonises the deep nasal passages. It's found in up to 80% of CIRS patients.
Why it matters: MARCoNS produces biotoxins that lower MSH (melanocyte stimulating hormone), an important anti-inflammatory neuropeptide. Until MARCoNS is treated, MSH stays suppressed and recovery stalls. You can take binders all day, but if MARCoNS is still active, it's fighting against your progress.
The standard treatment is BEG spray, a compounded nasal spray containing Bactroban, EDTA and Gentamicin, typically used twice a day for about a month. It's only started after VCS scores begin to improve from Step 2.
Where I am with this step
I haven't reached this step yet. It's ahead of me in the protocol and something I'll address once I've built up my Welchol tolerance and stabilised further. I'll share my experience when I get there.
Step 4Anti-gliadin antibodies
Some CIRS patients develop antibodies to gliadin, a protein found in gluten. This isn't the same as coeliac disease, but it still drives inflammation that can slow recovery. The treatment is typically a strict gluten-free diet for at least three months, followed by retesting.
Where I am with this step
This is one step I'd been doing long before I knew about the protocol. I mostly cut gluten out years ago, when I started taking a root-cause approach to my health - and the improvements were noticeable. My current diet is high animal-based and relatively low carb. However, living in South East Asia with an Indonesian wife, rice often ends up on my plate!
Step 5Correct androgens
CIRS can suppress hormones including DHEA, testosterone and oestrogen. This affects energy, mood, recovery and overall function, because the chronic inflammation interferes with hormonal signalling pathways.
Treatment involves hormone replacement or support as needed, guided by blood work. This isn't something you guess at - it requires testing to see what's actually out of range, then addressing those specific imbalances.
Where I am with this step
I haven't formally addressed this step yet. It's something I'll work through with my practitioner as I progress through the earlier steps.
Step 6ADH & osmolality
ADH (antidiuretic hormone) regulates water balance. CIRS can disrupt this, causing dehydration, excessive thirst, frequent urination or electrolyte imbalances. If ADH is too low, you can drink water all day and still feel dehydrated because your body isn't retaining it properly.
Treatment depends on the direction things are off. If ADH is low, DDAVP (desmopressin) may be prescribed. If ADH is elevated, water restriction might be needed.
Where I am with this step
Another step I haven't reached yet. I'll document my experience with it as I progress.
Step 7Correct MMP-9
MMP-9 (Matrix Metalloproteinase-9) is an inflammatory marker. When elevated, it breaks down tissue barriers and allows inflammatory compounds into places they shouldn't be - including the brain. This is one of the mechanisms behind the brain fog and neurological symptoms many CIRS patients experience.
The treatment is high-dose fish oil and a no-amylose diet - cutting starchy carbohydrates like bread, pasta, rice and potatoes.
Where I am with this step
I'm already on high-dose Omega 3s from my binder prep, so elements of this step are already in play. The no-amylose diet I haven't started yet. Something I'll need to address more seriously when I formally reach this step.
Step 8Correct VEGF
VEGF (Vascular Endothelial Growth Factor) controls blood vessel growth and oxygen delivery to tissues. When suppressed below 31 pg/mL, it causes fatigue, muscle cramps and poor recovery from exercise - one of the reasons many CIRS patients experience exercise intolerance.
The treatment is the same as Step 7: high-dose fish oil and the no-amylose diet.
Where I am with this step
I haven't had my VEGF levels formally tested yet. This is ahead of me in the protocol.
Step 9Correct C3a
C3a is part of the complement system, a component of the immune response. Elevated C3a can indicate the presence of bacterial membranes, sometimes linked to Lyme disease or its co-infections.
If C3a is elevated due to Borrelia (the bacteria that causes Lyme), antibiotics are used first to address the underlying infection. If levels remain elevated after that, a statin can be used to bring them down.
Where I am with this step
I haven't reached this step yet. I'll document my experience when I do.
Step 10Correct C4a
C4a is another complement marker and one of the key biomarkers used to confirm a CIRS diagnosis. It's often significantly elevated in CIRS patients and reflects the ongoing inflammatory load the body is dealing with.
C4a is addressed through the earlier protocol steps and eventually through VIP therapy in Step 12. It's not something that gets its own standalone treatment, but rather a marker that should improve as the other steps take effect.
Where I am with this step
This is ahead of me in the protocol. I'll update when I have blood work to share.
Step 11Correct TGF Beta-1
TGF Beta-1 is a growth factor that, when elevated, drives fibrosis, autoimmune-like symptoms and immune dysregulation. It's one of the more significant markers in CIRS.
The treatment is Losartan, a blood pressure medication used off-label at a lower dose (up to 25mg twice daily). A metabolite of Losartan called EXP3179 is what actually lowers TGF Beta-1.
A testing caveat
TGF Beta-1 is extremely sensitive to how blood samples are handled, processed and stored. Labs that aren't following the same protocols as the US reference labs can produce unreliable results, which makes testing outside North America or Australia particularly challenging. It's one of the biggest barriers for anyone pursuing a CIRS diagnosis internationally.
Where I am with this step
I haven't reached this step yet, and I'll need to navigate it carefully given the lab access challenges of living in Indonesia.
Step 12VIP therapy
VIP (Vasoactive Intestinal Peptide) is a neuropeptide your body naturally produces. In CIRS patients, VIP levels are often suppressed, which affects metabolism, immune regulation and brain function.
VIP therapy is the final step. It's administered as an intranasal spray, and the first dose must be given under practitioner supervision with blood work drawn before and 15 minutes after, to check for adverse reactions.
What makes this step significant is that, according to Shoemaker's research, VIP can correct multiple remaining markers at once - including C4a, TGF Beta-1, VEGF and MMP-9. It's the step that often brings everything together for patients who've worked through the earlier stages but still have lingering issues.
Where I am with this step
This is well ahead of me. But it's encouraging to know there's a powerful tool at the end of the process. I'll share my experience with VIP therapy if and when I get there.
Where I am right now
To summarise where I currently stand in the protocol:
- Step 1 (Remove yourself from exposure) is ongoing. My HERTSMI-2 score of 14 is on the higher end of borderline and I'm actively improving my environment with air purifiers, a dehumidifier, humidity tracking and daily ventilation.
- Step 2 (Binders) is where I am actively. I prepped with a two-week reset diet and high-dose Omega 3s, began at 1 Welchol tablet daily and I'm now up to 2 (recommended is 6). Brain fog has lifted noticeably.
- Step 4 (Gluten) has been in play for years without me knowing it was part of a protocol - I've been mostly gluten-free since my mid-twenties.
- Steps 3 and 5 through 12 are ahead of me. I'll document my progress (and update this blog) through each one as I get there.
The hardest part so far has been accepting that this isn't a quick fix. But seeing real improvements, even small ones, even in imperfect conditions, has given me confidence that the protocol works. If you're just starting out, don't let the length scare you. Focus on Step 1. Get your environment tested. Find a practitioner who understands CIRS. And take it one step at a time.
FAQ
How long does the CIRS protocol take?
Can you do the CIRS protocol without a doctor?
Is the Shoemaker Protocol the only treatment for CIRS?
Can CIRS come back after treatment?
Where can I get affordable CIRS treatment?
Where can I find a Shoemaker Protocol practitioner?
References
The information in this post is based on the following sources. I'd encourage anyone interested in CIRS to explore these for themselves.
- 1Dr. Ritchie Shoemaker. 12-Step Shoemaker Protocol Overview. The original protocol documentation from the physician who identified and developed the treatment for CIRS. https://www.survivingmold.com/docs/12_STEP_SHOEMAKER_PROTOCOL_FOR_CIRS.PDF
- 2Surviving Mold. Common Questions and Answers About Cholestyramine. Dr. Shoemaker's official resource covering CSM usage, dosing, side effects, and Welchol as an alternative. https://www.survivingmold.com/resources-for-patients/treatment/common-questions-answers-about-cholestyramine-and-why-its-the-most-effective-option-out-there
- 3Dr. Bruce Hoffman. 12 Steps of the Shoemaker Protocol. A detailed practitioner walkthrough of each step including treatment specifics and biomarker reference ranges. https://www.drbrucehoffman.com/post/shoemaker-protocol
- 4MoldCo. Decoding the Shoemaker Protocol: A Roadmap to Recovery. An accessible breakdown of the protocol from the telehealth platform where Dr. Shoemaker serves as Founding Physician. https://www.moldco.com/blog/decoding-the-shoemaker-protocol-cirs-a-roadmap-to-recovery
- 5Fatigue to Flourish. What is the Shoemaker Protocol? A comprehensive overview of each step with clinical context and references to Shoemaker's published research. https://www.fatiguetoflourish.com/what-is-the-shoemaker-protocol/
- 6Nutrition with Judy. Rx Binders vs. Natural Binders for CIRS. A detailed comparison of prescription binders versus natural alternatives, including molecular binding mechanisms. https://www.nutritionwithjudy.com/rx-binders-vs-natural-binders-for-cirs/
- 7CIRSMap. Binders and Detox Guide. Practical guidance on binder dosing, tolerance building, and preparation for sensitive patients. https://www.cirsmap.com/binders-detox-guide
- 8Park Compounding Pharmacy. Shoemaker and Brewer Protocols. A pharmacist's reference covering dosing, compounding options, and step-by-step treatment details. https://www.parkcompounding.com/shoemaker-and-brewer-protocols/
- 9Richmond Functional Medicine. CIRS Treatment Pathway Part 4. A clinician's guide to the treatment process including CSM/Welchol dosing schedules and MARCoNS management. https://www.richmondfunctionalmedicine.com/mold-related-biotoxin-illness-part4/
Not medical advice
I'm not a doctor or practitioner. I have no medical qualifications and nothing here should be taken as medical advice. This is one person's experience. Always do your own research and work with a qualified practitioner who understands your situation.
