6 min read
You finally connect the dots. Every time you leave town, the fog lifts. Every time you come back, your body crashes. It feels like you are living in a loop you cannot escape. It also sounds like you have been told a dozen times that it is stress or anxiety.
It makes sense if you feel both relieved and terrified. Relief because there is a name for it. Terrified because you want a plan that is real and structured, not another vague wellness checklist.
The Shoemaker Protocol is that structured plan. It is a stepwise treatment framework for Chronic Inflammatory Response Syndrome, or CIRS, that was built from clinical research in people exposed to water-damaged buildings. It is not a quick fix. It is a sequence that protects your body from getting stuck in the wrong order.
18 of 21
Participants with abnormal VCS
Water damaged building study showed visual contrast deficits that improved with treatment
Up to 25%
Estimated susceptibility
Review noted a sizable portion of the population may be vulnerable to CIRS
## What the Shoemaker Protocol Actually Is
This protocol is not one supplement or one test. It is a clinical roadmap designed to remove exposure, clear biotoxins, and then calm the immune and hormonal chaos that follows. The sequence matters because each step affects the next one. If you try to correct hormones before removing toxins, the inflammation usually wins.
The backbone of this approach comes from time series and clinical trial research in people exposed to water damaged buildings, including the studies that tested cholestyramine as a binder and documented relapse with reexposure [Shoemaker 2005](https://doi.org/10.1016/j.ntt.2004.07.005) [Shoemaker 2006](https://doi.org/10.1016/j.ntt.2006.07.003). A more recent review summarized the evidence for treatment efficacy and emphasized that CIRS is underrecognized [Dooley 2024](https://pubmed.ncbi.nlm.nih.gov/39649915/).
If you want a clear foundation before diving into treatment, start here: [CIRS Explained](/vault/understanding-cirs).
It sounds like you have been trying to recover while still being exposed. That is not a personal failure. The protocol is built on the idea that exposure control comes first.
## The Science Behind the Sequence
CIRS is an innate immune response that does not shut off. Biotoxins from water damaged buildings can keep inflammatory pathways turned on, and in some people, the body does not tag and clear those toxins effectively. That ongoing signal can disrupt hormones, blood flow, sleep, cognition, and mood. It is why your symptoms feel like they jump from system to system.
The Shoemaker studies describe a repeatable pattern. People exposed to water damaged buildings had multi system symptoms, abnormal visual contrast sensitivity, and improvements after cholestyramine therapy plus avoidance. Then symptoms flared again with reexposure [Shoemaker 2005](https://doi.org/10.1016/j.ntt.2004.07.005). That cycle is not psychological. It is observable and measurable.
The protocol follows that biology. Remove the trigger, bind what is recirculating, treat ongoing colonization in the sinuses, then address the downstream markers in order. That is why it feels so linear even when your symptoms are not.
## Why This Gets Missed
Many people are told they have allergies, anxiety, or chronic fatigue. Those labels can overlap with your symptoms, but they miss the core mechanism of biotoxin driven inflammation. A modern review highlights how often CIRS is misdiagnosed and how a stepwise treatment plan is more effective than random symptom chasing [Dooley 2024](https://pubmed.ncbi.nlm.nih.gov/39649915/).
✅ CIRS pattern
- Multi system symptoms that cluster and shift
- Worse indoors, better when away
- Abnormal VCS or inflammatory markers
❌ Simple allergy pattern
- Mostly eyes, nose, lungs
- Responds to antihistamines alone
- No relapse pattern tied to buildings
If you have not evaluated your environment yet, this is a good next step: [Testing Your Home for Mold](/vault/testing-your-home-for-mold).
## The Shoemaker Protocol, Step by Step
Below is the classic sequence. Your clinician will tailor it, but the order is the heart of the method.
This is non negotiable. Remediate, relocate, or create a safe room. Even a perfect treatment plan cannot outpace ongoing exposure.
Cholestyramine or Welchol can bind biotoxins in the gut so they can be eliminated. This is the most studied intervention in the protocol [Shoemaker 2006](https://doi.org/10.1016/j.ntt.2006.07.003).
MARCoNS is a resistant staph colonization in the sinuses. It can keep inflammation active and must be cleared with targeted therapy if present.
If antibodies suggest gluten driven inflammation, diet and gut repair come next.
DHEA and testosterone can drop or dysregulate in CIRS, which affects energy and recovery.
Hydration and electrolyte regulation are often off. Normalizing ADH can reduce thirst, frequent urination, and lightheadedness.
MMP 9 reflects ongoing inflammation and vascular stress. It is addressed after biotoxin clearance.
VEGF supports blood flow and oxygen delivery. Low levels can contribute to fatigue and pain.
Complement activation is another sign of immune overdrive. This step targets that pathway.
This complements the previous step and helps settle persistent inflammation.
TGF beta 1 is a cytokine involved in tissue remodeling and immune balance. It often stays high in CIRS.
VIP is the final step for many patients. It is only started when exposure is controlled and labs are stable.
Skipping steps or jumping ahead can backfire. The protocol is designed to calm the immune response in the correct order.
If you want a detailed breakdown of binders, see [Detox Binders Explained](/vault/detox-binders-explained). For environment control, [Creating a Safe Room](/vault/creating-a-safe-room) can make a real difference when relocation is not possible.
## Practical Steps You Can Take Right Now
You do not need to do everything today. You do need a clear starting point. Here is a grounded path you can take even before you find the perfect clinician.
- Start a symptom journal with dates, places, and exposures
- Schedule a professional mold inspection or ERMI test
- Run a VCS test as a low cost screening tool
- Gather past labs and imaging to share with a CIRS aware doctor
- Reduce exposure in the rooms where you sleep
You deserve someone who understands this framework. This guide can help: Finding a Mold Literate Doctor.
## Common Questions People Ask
**Is the Shoemaker Protocol the only way to recover?**
No. It is the most documented and structured approach, but some clinicians blend it with functional medicine, nutrition, and additional detox strategies. What matters most is that your plan follows the logic of exposure control and stepwise immune recovery.
**How long does it take?**
It varies. Many people need months, not weeks. The pace depends on how quickly you can control exposure, how your body responds to binders, and how many markers are out of range.
**Can I do this alone?**
This is not a DIY protocol. It requires lab monitoring and clinical supervision. If you feel stuck, focus on the parts you can control right now and bring that information to a practitioner.
## Encouragement for the Long Haul
It sounds like you have been in survival mode for a long time. That is exhausting. The Shoemaker Protocol is not a judgment of how you got here. It is a map out.
You do not have to believe in everything all at once. You just have to take the next right step. Start with your environment. Document your pattern. Find a clinician who listens. Recovery is not linear, but it is possible.
The Shoemaker Protocol works because it follows the biology of CIRS in the right order: remove exposure, bind biotoxins, then correct the downstream immune and hormone disruptions.
### Read next
– [CIRS Explained](/vault/understanding-cirs)
– [Testing Your Home for Mold](/vault/testing-your-home-for-mold)
– [Creating a Safe Room](/vault/creating-a-safe-room)
– [Finding a Mold Literate Doctor](/vault/finding-mold-literate-doctor)
## Sources
– [Shoemaker 2005](https://doi.org/10.1016/j.ntt.2004.07.005) A time series study of sick building syndrome and biotoxin associated illness
– [Shoemaker 2006](https://doi.org/10.1016/j.ntt.2006.07.003) Clinical trial of cholestyramine in water damaged building exposure
– [Dooley 2024](https://pubmed.ncbi.nlm.nih.gov/39649915/) Review of evidence for CIRS treatment efficacy