The Case for Measuring the Illness: Pros and Cons of the Shoemaker Protocol

Note: This is part 1 of 4 of a series of blogs where I map the major thinkers in CIRS and mold-related illness: what each one believes, where each one excels, and where each one breaks down.

Introduction: I argued that the four major camps aren’t actually contradicting each other. Each one is answering the same question in a different way: Where is the illness?
Part One: Does the Shoemaker Protocol Work? This post looks at the camp that addresses the question scientifically.

*Note: this blog was written by me, Mark Volmer. All spelling mistakes, misquotes, errors, and omissions are my own doing. It is not AI generated. *

I’ll start by noting that I am a certified Shoemaker Protocol Practitioner. The framework I use to treat a CIRS patient is primarily based on what I’ve learned from Dr. Shoemaker. So when I tell you about the limits of the Shoemaker Protocol (What is the Shoemaker Protocol?), I’m not throwing stones from outside. I’m telling you what I’ve run into from the inside, with real patients, moving them through actual treatment.

Expert Recap: Does the Shoemaker Protocol work?

The Shoemaker Protocol is the only scientifically proven method of treating Chronic Inflammatory Response Syndrome (CIRS). Dr. Shoemaker has created a method to diagnose it and reverse it. This method is called the Shoemaker Protocol, and it’s based on a pyramid. Each step of the pyramid must be addressed before moving on to the next. The most important step is the first, which is removing exposure.

What the Shoemaker Protocol does not take into account is that many patients are too ill to even start the protocol. The protocol also relies on expensive testing, making it out of reach for many chronically ill patients.

The Shoemaker Point of View

Recall the question from the introduction to this series: Where is the illness?

Dr. Ritchie Shoemaker’s answer is the most precise in the field:

The illness is not the mold. The illness is your body’s response to the mold.

In people who are genetically susceptible, exposure to biotoxins from a water-damaged building triggers the innate immune system to switch on and then fail to switch back off. That sustained, self-perpetuating inflammation is the disease. Dr. Shoemaker named it Chronic Inflammatory Response Syndrome (CIRS), and over the course of more than two decades he built a framework to:

Diagnose CIRS
CIRS can be diagnosed by testing Inflammatory Markers, or using information from the GENIE test
Reverse it
The Shoemaker Protocol is scientifically proven to treat and reverse CIRS

Proven Causes of CIRS

More recently, CIRS research has exploded. For years, we thought mold was the primary driver of this illness. As it turns out, mold is only the fourth most common cause of CIRS. The main causes of CIRS are:

Actinomycetes
Endotoxins
Beta Glucans
Mold

The mention of biotoxins other than mold is something only Dr. Shoemaker mentions and includes in his treatment recommendations. Practitioner Dr. Jill Crista, very recently introduced the concept of Actinomycetes to her followers. However, her information on this topic was little more than a cursory introduction (more on that in the next blog). The exploration on what specific biotoxin drives the illness is uniquely Shoemaker.

The Importance of Correct Home Testing

If you are someone who did not respond to treatment, the first place I always recommend looking is a hidden ongoing exposure.

Which biotoxin(s) did you evaluate in your home environment?
How did you evaluate your environment for this biotoxin(s)?

Petri dishes, surface swabs, and/or air samples are not enough for CIRS. A HERTSMI-2 or ERMI is the gold standard mold testing for the CIRS crowd. But those only test for mold. If your HERTSMI or ERMI looks good but you’re not making any progress in treatment, further evaluation for endotoxins, actinomycetes, or beta glucans often reveals why you’re stalled.

The defining feature of Dr. Shoemaker’s framework is a refusal to guess. Dr. Shoemaker insists that CIRS leaves fingerprints you can measure:

A recognizable pattern of inflammatory markers,
Hormones thrown out of their normal relationships,
Most recently, a specific signature in how your mitochondrial genes are being expressed.

This is the heart of CIRS. Dr. Shoemaker turned a mystery illness into something you can prove a person has. And just as important, he created a way to prove a person no longer has it.

Why Dr. Shoemaker’s work matters

In most of the chronic illness world, “better” is a feeling. The patient reports they have more good days. Great. We need that. But it also can’t be proven. It leaves both patient and practitioner vulnerable to wishful thinking, placebo, and the slow drift of moving goalposts.

The testing Dr. Shoemaker came up with provides impartial evidence. The inflammatory markers either normalized or they didn’t. The gene expression either corrected or it didn’t. You may be feeling better, but if the evidence shows that illness is present, we know that treatment is not yet complete.

On the other hand, you can have a patient who legitimately does not feel better but the labs say the fire is out. This means it’s time to go looking for what else is wrong.

Either way, you’re not flying blind.

For a patient who has spent years being told their bloodwork is “normal” and the problem is in their head, these labs can be life changing. Time and time again I have showed a patient positive test results and they cry tears of joy. It’s not that they’re happy to be sick; it’s validation that what they’re living is real. The testing Dr. Shoemaker created is proof that the issue is in their mitochondria and their innate immune system.

More strengths of the Shoemaker Protocol

A few more things Dr. Shoemaker gets right, and gets right better than anyone else:

1. The Shoemaker Protocol respects sequence.

The protocol is built in a deliberate order. The first step, which is removal from exposure, comes first for a reason. There is no point trying to put out a fire while someone keeps pouring gas on it. A lot of mold treatment fails, not because the tools are wrong, but because they’re applied in the wrong order. I have never seen a patient recover from CIRS while still living in a water damaged building. The Shoemaker Protocol demands removal from exposure first, and before proceeding through the protocol, for good reason.

2. The Shoemaker Protocol is published and reproducible.

Whatever its limits, the Shoemaker Protocol is the only treatment in the mold-illness space that has been peer-reviewed. This means that different practitioners can follow the steps and get comparable results. You can take your lab results to any Shoemaker-trained practitioner and you’ll get the same answer: You either have CIRS or you don’t.

The fact that this protocol can be reproduced is an incredible strength. It legitimizes the entire protocol.

3. It takes susceptibility seriously.

The insistence that some people are genetically primed to get sick from exposures that others shrug off was, for a long time, treated as fringe. But Shoemaker explained, Why me and not my spouse? The answer was in your genes.

4. It knows that the key to success is managing exposure.

No one else has put in the work like Dr. Shoemaker when it comes to identifying, evaluating, maintaining and creating a CIRS-safe environment. If not for Dr. Shoemaker, we’d have no idea how to test a home for mold, actinomycetes, or endotoxins. You can thank Dr. Shoemaker for the environmental protocols for CIRS. With the help of environmental experts we have created a robust literature on what standards need to be met for CIRS-safe housing. And because of this, we’ve created protocols and best-practices on how to remediate a home.

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Where the Shoemaker Protocol Struggles

Here’s where I have to be honest about what I run into.

The strict rules that make the protocol so powerful are the same thing that makes it unforgiving. The protocol assumes a patient can tolerate the protocol. And a meaningful slice of the sickest patients — often the sickest ones — are not able to tolerate the protocol.

Let me describe the patient I mean, because she’s real and I see her often. This patient is:

Profoundly reactive.
Her mast cells are on a hair trigger.
Her nervous system is locked in a defensive state where almost any intervention reads as a threat.

When this patient attempts the second step of the protocol and tries to take a binder, she doesn’t slowly improve like other patients. Instead, she crashes, hard, sometimes for weeks. The very thing that’s supposed to start her recovery is something her body experiences as an assault.

The Weakness of the Shoemaker Protocol

If the Shoemaker Protocol is strictly followed, it has a limited answer for the sickest patients. The protocol is a sequence, and if a patient can’t get through step one, the sequence stalls. You can lower doses and slow down — good practitioners do — but the underlying assumption is still that the patient’s job is to tolerate the protocol, rather than the protocol’s job to meet a patient who can’t.

This is the fault line that matters most, and it’s worth being precise about what kind of failure it is. It is not that Dr. Shoemaker is wrong. The biology he describes is, as far as I can tell, accurate. The markers are real. The sequence is sound. It’s that the protocol was built to answer one question: What is the inflammatory illness and how is it staged and reversed?

It answer this question superbly well.

However, it does not address those patients who are not able to even begin the protocol.

Other cons of the Shoemaker Protocol

A few smaller fault lines worth naming honestly, which I’ll take up in more depth later in the series:

The genetic story is more contested than it’s often presented. The HLA-DR susceptibility framing is foundational to the classic model, but other serious clinicians argue it’s far from settled. There are plenty of sick patients who don’t fit the genetic predictions. This doesn’t collapse the framework, but it does mean the genetic gatekeeping should be held a little more loosely than the strictest reading suggests.
It is demanding, slow, and expensive. The testing is extensive and not cheap. The protocol can run for a year or longer. Binders, the early workhorses of the protocol, are poorly tolerated by a real fraction of patients. None of this makes it wrong — serious illness sometimes demands serious effort — but it does put the full protocol out of reach for some of the people who need it.

But does the Shoemaker Protocol work?

I want to end where I started: this is the framework I trust most as a foundation. When a patient walks in, the Shoemaker model is how I figure out whether they actually have CIRS, how sick they are, and whether the treatment is working. The objectivity it demands is a discipline I wouldn’t give up.

But a foundation is not a finished house. The patients who find their way to a clinic like mine are very often the ones for whom the protocol, run by the book, already stalled — the reactive, the hypersensitive, the ones whose systems won’t let them through step one. Treating them doesn’t mean abandoning Shoemaker’s map. It means recognizing that the map is exquisitely detailed about the territory it covers, and quieter about the territory just past its edge.

That edge — the patient who can’t tolerate treatment — is exactly where the next camp lives.

Next in the series: Dr. Neil Nathan and Dr. Jill Crista, and the case that the real bottleneck isn’t the illness at all — it’s whether the patient can be treated in the first place.