The 8 Autoimmune Systems We Need To Talk About in Functional Medicine

The 8 Autoimmune Systems We Need To Talk About in Functional Medicine Dr. Will Cole

Autoimmune problems in America are growing by leaps and bounds with close to 50 million people living with a diagnosed autoimmune condition. But that’s just the tip of the iceberg - autoimmune conditions are the end stage of the larger autoimmune-inflammation spectrum.

In order to be diagnosed with an autoimmune disease, your body has had to destroy a significant amount of tissue. That’s why I see many people in my telehealth functional medicine clinic who have struggled for years with “unexplained” symptoms before getting diagnosed with autoimmunity.

This is because inflammation typically starts out small with “common” symptoms like fatigue and weight gain on its way to destroying your body. It’s my goal to uncover chronic inflammation and stop it before it goes on for too long.

One way to do this is by understanding where inflammation can manifest in the body as it can vary between individuals. In my book, The Inflammation Spectrum, I take a comprehensive look at the autoimmune-inflammation spectrum, how you can identify inflammation in your body, and what you can do to win the battle against inflammation through food and other wellness tools. But for now, let's take a look at the areas that I recommend monitoring for inflammation and possible autoimmunity:


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1. The digestive system

Most people struggling with chronic health problems have some level of inflammation in their gut. This can lead to problems like constipation, bloating, diarrhea, acid reflux, SIBO, and food intolerances. If this inflammation is not addressed it can lead to leaky gut syndrome that can result in gut-related autoimmune conditions like Crohn’s disease, autoimmune gastritis, or Irritable Bowel Syndrome (IBS).

2. The brain and nervous system

Symptoms like brain fog, fatigue, anxiety, poor memory, and irritability can all be signs of inflammation in the brain that can increase your risk for dementia (1) or neurological diseases like Parkinson’s.

This all goes back to your blood-brain barrier. The same proteins that control your gut permeability also control the permeability of your blood-brain barrier. When this happens, bacterial endotoxins end up leaking into your bloodstream causing a cascade of inflammation to your brain.

3. The detoxification system

Your detoxification system - liver, kidneys, gallbladder, and lymphatic system - are responsible for removing toxins from your body like pesticides, mold, heavy metals, alcohol, and waste from your own metabolism. Inflammation can inhibit your detoxification system and cause a build up of toxins in your body. This ends up perpetuating inflammation and creates a vicious cycle of inflammation and toxin build up. Rashes, swelling, and skin problems are all signs that your detoxification system isn’t working well.

4. The endocrine system

Your endocrine system is your body’s communication system between your brain and the glands that produce hormones. When inflammation occurs in this area, it can inhibit proper production of hormones of your thyroid, sex glands, or adrenal glands. Since your hormones are considered the chemical messengers of your body, instructing every area of your health, when they aren’t functioning well, chances are not much else is either. Symptoms of hormone imbalance and inflammation in this area can include anxiety, irregular menstruation, low libido, thinning hair, or weak nails.

5. Blood sugar and insulin system

If you are hangry between meals, always thirsty, have sudden weight gain, have trouble losing weight, or have high fasting blood sugar numbers, you likely have high inflammation in this area. Your blood sugar and insulin system are controlled by your liver, pancreas, and cellular insular reception sites. Out-of-control inflammation can result in unstable blood sugar (2) that can lead to metabolic syndrome, prediabetes, and even Type 2 diabetes. (3)

6. The musculoskeletal system

Your muscles, joints, and connective tissue all make up your musculoskeletal system. Joint pain, muscle aches, joint stiffness, and fibromyalgia are all signs that you have inflammation in this area.

7. The immune system

Your immune system is the governing system over inflammation. Autoimmunity happens when your immune system overreacts, causing a cascade of inflammation that attacks your organs, tissues, and structures of your body. Ultimately, each one of the systems I mentioned can be affected by autoimmunity with your symptoms being the first signs of that autoimmune-inflammation spectrum in action.

8. Polyinflammation

Inflammation rarely happens in just one area of your body. In fact, inflammation typically occurs in multiple systems of your body. That’s why a lot of people with one autoimmune condition have a higher likelihood of developing another.

Next Steps

All this to say, it’s vital that we manage our inflammation levels so we don’t end up on the path to autoimmunity. By running labs and working with a functional medicine expert, you can identify to what extent inflammation resides in your body and take the proper steps to manage it. 

I created The Inflammation Spectrum quiz to help you determine if and where inflammation might be affecting your health. If you are ready to take your healing journey even deeper, check out my telehealth functional medicine consultation to learn more about how we can help you address inflammation with functional medicine.

As one of the first functional medicine telehealth clinics in the world, we provide webcam health consultations for people around the globe.


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  1. Sartori, Andrea C et al. “The impact of inflammation on cognitive function in older adults: implications for healthcare practice and research.” The Journal of neuroscience nursing : journal of the American Association of Neuroscience Nurses vol. 44,4 (2012): 206-17. doi:10.1097/JNN.0b013e3182527690
  2. Tsalamandris, Sotirios et al. “The Role of Inflammation in Diabetes: Current Concepts and Future Perspectives.” European cardiology vol. 14,1 (2019): 50-59. doi:10.15420/ecr.2018.33.1
  3. de Candia, Paola et al. “Type 2 Diabetes: How Much of an Autoimmune Disease?.” Frontiers in endocrinology vol. 10 451. 4 Jul. 2019, doi:10.3389/fendo.2019.00451

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Dr. Will Cole, DNM, IFMCP, DC is a leading functional medicine expert who consults people around the globe, starting one of the first functional medicine telehealth centers in the world. Named one of the top 50 functional and integrative doctors in the nation, Dr. Will Cole provides a functional medicine approach for thyroid issues, autoimmune conditions, hormonal imbalances, digestive disorders, and brain problems. He is the host of the popular The Art Of Being Well podcast and the New York Times bestselling author of Intuitive Fasting, Ketotarian, The Inflammation Spectrum and the brand new book Gut Feelings: Healing the Shame-Fueled Relationship Between What You Eat and How You Feel.