Active Autoimmunity and Chronic Tissue Damage

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 a 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 two articles, I discussed Stage One – An Erratic and Reactive Immune System and Stage Two – A Stubborn and Tired Immune system. If you have not read those articles yet, tap the appropriate link below.

The Five Stages

In this article, I am going to introduce you to Stage Three.

If the following experience sounds familiar, I encourage you to look into the Ancestral Autoimmune Protocol for Stage Three (See Below)

Stage Three – Active Autoimmunity and Chronic Tissue Damage

For you to be in Stage Three of the Autoimmune Spectrum, you need to be diagnosed with a fixed name, possibly lifelong, Autoimmune Condition.

At this point, you will probably have taken antibiotics, painkillers and/or antidepressants, antiinflammatories, and possibly even immune-suppressing steroid drugs. Your doctor will begin treating you as if you will be spending a lot more time together.

Autoimmunity is like a bad marriage. Imagine being in a marriage that has become a long grind of just trying to control the damage. You have both become masters of the slow burn, pushing each other’s buttons but not pushing anyone out of the door. At least, not yet!

In Stage Three, you will need to find the balance of minimal stress and a lifestyle dedicated to healing your immune system.

In this stage of Autoimmune disease, your whole body is now in a pitched battle. Although it may only appear to be going after your hair, your gut, your skin, or your elbow, the upregulation in immune system activity can change your entire metabolism.

This can change your mood, your sleep, your memory, or even your sex drive.

The most important change is almost unconscious. Your life’s sense of meaning may go from ‘How good can I make it?’ to, ‘How bad can I take it?’

The Autoimmune Spectrum is meant to help patients and clinicians find some sense of predictability in a highly chaotic situation. I have met people in Stage Three who had no previous medical history. I have also met people who had every symptom of Stage One and then Stage Two, starting the day they were born.

My preference and goal, when I meet patients in Stage Three, is to help them return to Stage Two, then Stage One and then have normal health. I have also worked with people whose condition progressed rapidly or moved on to include other Autoimmune Conditions.

All any of us can do is be VERY thorough in our assessment of our health and then do EVERYTHING we can to get better.

In Stage Three, your primary concern is simple – DO NOT enter Stage Four.

Your next job is to work your way back to Stage Two.

Autoimmunity is a life-long process. Some of us have decades of good health and some of us just want one good day. To turn this around, you will need to become one of those people who doesn’t eat everything you are offered. You may even become one of those people who starts sharing leading-edge medical research at a dinner party.

You will definitely want to become one of those people who takes a handful of supplements every day – at least, at first.

The hardest part for us all is having to change most of our habits.

Stage Three ~ 120 Days

If you have been diagnosed with an active Autoimmune Disease, your life has just changed -possibly forever.

That change might be very little in the long term, but in the short term, you will want to become focused on a specific, step-by-step, four-month protocol. There are a few options, but they are all similar in focus and intended outcomes.

Before I describe my approach to this stage of Autoimmunity, I want to bring your attention to how impatient, and hyperfocused this can make people feel.

I often relate this process to training an injured puppy. How many times a day do you need to sit on the floor and take care of your puppy, however it is doing and whatever it has been chewing or peeing on.

At the beginning of this process, we all need to accept that this relationship is up to how badly your immune system puppy has been treated throughout your life. This analogy isn’t really about a puppy. It is meant to bring your attention to the kind of trainer you plan to be.

The Ancestral-AIP is intended to change the way your immune system behaves. Over a long time. Depending on many factors. Your best bet is to focus on consistency and patience. You cannot make a puppy comfortable by yelling at it.

This is going to take time.

In my experience, it takes a minimum of four months to down-regulate an active Autoimmune process. It can take two years, but four months is effective for many of my patients. There are some immune system characteristics that give this period of time some theoretical credibility. See the article, Functional medicine and Autoimmunity.

As a patient with Crohn’s Disease and Colitis, I stick to a Stage Three Protocol most of the time. Symptomatically I fall into an early Stage Two of Spectrum.

If I feel like I am moving into an active Stage Three Autoimmune Flare-Up, I automatically commit four months to a diet centred around smoothies, stews, curries, stir-fries, casseroles, and occasional salads.

How strict your diet needs to be, depends on the intensity and momentum of your unique Flare-Up. 

This is the point and the importance of seeing Autoimmune Dysfunction as a spectrum.

No matter what is on the menu, I make the most creative and delicious food I can dream up because it is so much more enjoyable and worth it for everyone. Like many others on these kinds of protocols, or like people focused on fitness or modelling, we all start to fall in love with batch cooking. If you are new to staying several days ahead in the kitchen, check out this article – Batch Cooking Saves Lives!

In Stage Three, you will have to be very patient and organized.

That is honestly the biggest challenge people face. This will take four months and you may need to repeat this protocol every few years, or after times of severe stress.  Try and think of this as a new family tradition and give yourself permission to be as creative and engaged as possible.

In my experience as a patient and as a clinician, 2 – 3 weeks on the Phase One Protocol resets the inflammatory status of the immune system. If there are no changes then a more advanced protocol is advised – see your clinician.

The short term use of Pharmaceuticals may be necessary.

In Stage Three you want to have regular conversations with your Doctor and an Integrative, TCM or Functional Medicine practitioner. Your health team will be able to guide you as to the best supplements and lab-tests to get you started on the journey to restoring your immune system. That usually starts by repairing the damage from chronic inflammation.

The Phase One Diet is all about reducing inflammation and sending a very strong message to your brain, organs, genes and epigenetic pathways.

My next recommendation, if approved by your clinician, would be a very nutrient-dense Phase Two Diet. This protocol focuses on a combination of High Collagen foods, intermittent fasting, or a Ketogenic Diet.

If you are catabolic, (have recently lost a lot of weight), then fasting is not for you!

There are a few other situations that would make this challenging so please talk to a knowledgeable clinician and make sure fasting of any kind is a good idea.

If you are confident this is safe, then follow the basic intermittent fasting protocol. A standard cycle is to fast for 16 hours, keeping your feeding opportunity to a strict 8-hour window. This would allow you to eat from 10:00 am to 6 pm.

If you start losing weight that you do not want to, then increase your healthy roots and eat with a focus on maintaining your weight.

Keep in mind that many Autoimmune conditions begin with a period of gradual and potentially dangerous weight loss. If you are losing weight, you may need to interrupt your immune system or tranquillize that VERY dangerous and angry dog (that could literally eat you alive) with some immune suppressant drugs.

This has saved my life a few times, and it is sometimes a perfect place to start. In Stage Three, you will likely (or should) be taking immune stabilizing supplements three times per day. The use of supplements is described in the articles of the Four Phases of the Ancestral-AIP.

After six weeks to three months, if you are doing well and your clinician agrees, it may be a good time to test the resilience of your immune system. If the Autoimmune flare has settled, some people are ok with nightshades, eggs, and a few nuts. I do not usually suggest this before 100 days, but there are always exceptions.

Stage Three Autoimmunity requires a Progressive Ancestral-AIP.

      • Two to Three Weeks on the Phase One (Anti-inflammatory) Protocol.
      • Six to eight weeks on the Phase Two (High Collagen and High Fibre) Protocol.
      • If you are not feeling better after 2 months, go back to Phase One and repeat until your immune system responds.
      • If you are feeling better then try a nightshade and/or egg challenge. If you respond well – gradually shift to Phase Three
      • Stay on the Phase Three Protocol until your symptoms and lab tests agree that you are healthy and stable.
      • Move onto Phase Four, but have a Phase One week anytime you feel ‘off’.

To avoid another flare-up,  I recommend a two-month reset with a focus on cleansing every year.

Ancestral Autoimmune Protocol


If you have not read these articles,

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


I want to begin my Autoimmune Healing Journey

Please send me a FREE copy of the Autoimmune Protocol Ebook!

Begin your healing journey with this 65-page guide to understanding Autoimmune Disease and the Ancestral approach to restoring healthy immune function from the inside out.

Sign up for a regular newsletter offering you the information and inspiration that has helped thousands of people heal their lives!

    We respect your privacy.

    You will only receive your FREE Ebook and our newsletter.

    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.