The Five Stages of Autoimmunity

In this series of articles, I am exploring the Autoimmune Spectrum.

If you have been diagnosed with an Autoimmune Condition, I am sorry to hear that. I encourage all of my patients to think of their diagnosis as a description (or label) for a complex process.

It is a good start, but a diagnosis rarely describes the severity, momentum, and degree of immune system reactivity.

In the previous article, I discussed Stage One – An Erratic and Reactive Immune System. If you have not read that yet, tap here.

The Five Stages

In this article, I am going to introduce you to Stage Two. If this experience sounds familiar, I encourage you to look into the Ancestral Autoimmune Protocol for Stage Two. (See Below)

Stage Two – A Stubborn and Tired Immune System

I often use the metaphor of a dysfunctional marriage to describe Autoimmunity. If your imaginary marriage is continuing to spiral into dysfunction, you can expect two things to happen.

First, you will become familiar with the fatigue of a futile struggle.

Second, you will find yourself locking horns and trying to win – you probably won’t even remember why.

I use this metaphor to bring your awareness to that quality of experience. Stubborn and tired. Your immune system is unfortunately very good at that style of argument. If you feel that way, and your symptoms feel that way, take advantage of this opportunity to turn your immune system marriage around.

You DO NOT want an Autoimmune Disease if you can prevent it!

The Second Stage of Autoimmunity can be described as Pre-Autoimmune Syndrome or Hidden Autoimmunity.

Most of the people suffering from this level of immune system dysfunction have had lingering symptoms like:

      • Chronic Pain
      • IBS
      • Insomnia
      • Symptoms come and go in severity
      • Symptoms that never resolve
      • Low energy
      • Low mood
      • Slow wound healing
      • Poor exercise recovery

In my experience, when a person has a considerable history of Stage One symptoms like seasonal, dust, or pet allergies, exercise-induced Asthma, or Eczema, or chronic infections, and also presents with chronic and lingering symptoms that are not responding to normal treatment, their immune system is stuck in an argument that will eventually exhaust all of their resources. Unless they turn their immune system around.

This may produce chronic physical and/or mental health challenges, and even some chronic diagnosable conditions that are not associated with Autoimmunity.

Why is this stage included if it is not clinically an Autoimmune condition?

Simply, because so many people with clinically diagnosable Autoimmune Diseases spend a few years unconsciously encouraging their immune system to become more stubborn and aggressive. People in Stage Two have usually tried a few medications to control their most limiting symptoms. Unfortunately, these medications often mask the progress of deeper immune system dysfunction.

If you carry the genes for an Autoimmune condition and cannot regulate this kind of ‘slow-burn’ momentum, this diagnosable condition will eventually turn on.

Take Irritable Bowel Syndrome (IBS) for example. IBS is the most common reason that patients are referred to a Gastroenterologist.

For some people, IBS is triggered by a strange list of seemingly unrelated foods, for others, it is poor sleep, and for others, it is always chronic stress. After years of poor digestion, mild malnutrition, and chronic immune system distress, many patients develop active Autoimmune conditions like Crohn’s Disease, Ulcerative Colitis, Asthma, Rheumatoid Arthritis, or one of the chronic conditions that run in their family.

Butting your head against the triggers and stressors that make your immune system more aggressive, or your inner marriage more stubborn and exhausted may push you into Stage Three. If you are not able to control your choices or your level of stress, try Acupuncture or any other therapy that changes your state of being and helps reduce any cravings.

If you can be consistent with your choices, with or without help, you may be able to reorient your immune system and health in approximately two months.

This is why the Autoimmune Spectrum is organized the way that it is.

When I first meet a new patient with Hidden of Active Autoimmunity, within a few minutes of asking questions I usually have a clearer idea of how long this person may need to restrict their diet and modify their lifestyle.

And, more importantly, it becomes clearer exactly which long term protocol is the most likely to produce effective results.

Stage Two  – Two Months

This kind of immune system grudge is difficult to treat because it often involves many systems in your body. I always encourage some basic lab tests to see which systems are under the most distress.

Talk with your Functional medicine clinician about getting these tests:

      • Cortisol and DHEA balance – The Dutch Test is my favourite.
      • Intestinal Permeability Test
      • Mediated Release food intolerance test
      • Oxidative Stress and Lipid Peroxide test
      • Intestinal Pathogens Test
      • Organic Acid Test (OAT)

In Stage Two, you have to calm your immune system and give it some time to learn a new and better way to be in the world and in your body.

In most cases, it is safe to do a broth fast for one day (24 hours) every week. Even if you are eating the healthiest food you can find, the basic process of digestion can be an immune system irritant. Learn more about the benefits of fasting and intermittent fasting HERE

If not eating for 24 hours sounds like more stress than you can adapt to right now, then I encourage you to consider intermittent fasting.

In Stage Two, you don’t want to stress your body very much, so an intermittent fasting cycle of 16 hours fasting, with an 8-hour feeding window, is ideal. To keep your metabolism stable, eat three times a day once per week.

Start Here: Focus on a Phase Two diet for one month and then the Phase Three diet for the next month.

If you have a condition that is highly inflammatory or have Autoimmune conditions in your family, you may get better results if you begin with one or two weeks of the Phase One  Protocol.

I would also encourage you to get a health journal and keep track of your diet, sleep, stress and symptoms. There several online APPs that are free if you are engaged with modern technology. A pen and paper will always work!

If you have had your condition for more than two years, then invest two months every year doing the same protocol with a focus on detoxification. If you want some support and accountability with that process, I host an online Autoimmune Reset and Cleanse twice a year.

The last suggestion I have for anyone in Stage Two is to find a mentor about health and fitness.

Find someone that excites you about your own health. I believe that we should all have to go to a gym class every year as a part of our health insurance. Yoga is on every street corner for a reason. If you are new to practices like Qi Gong and Meditation, they are worth every second you spend learning and practicing them. You can learn more about the proven benefits of Qi Gong HERE!

I would also encourage you to seek out a local health detective who can help you discover the root cause of your situation.

Here are a few questions I ask patients in Stage Two:

What is the value of your long-term health?

How much of your energy and time is taken up with this illness process?

On a scale of one to ten, how committed are you to changing your health and your life?

Ancestral Autoimmune Protocol


If you have not read these articles,

they may have some important answers, perspective, and guidance.


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    Michael Smith is an internationally respected Clinician, Author, and Speaker.

    Michael practices Functional Medicine, Acupuncture, and Traditional Chinese Medicine, and encourages his patients to follow an Ancestral approach to lifestyle and diet. Dr. Smith has dedicated the last 25 years to the research and treatment of Chronic Illness and Autoimmune Disease. As an Autoimmune patient, Michael is intimately aware of the devastating impact these conditions can have on your quality of life.