How to Test for Autoimmune Triggers & Root Cause

So you’ve got an autoimmune disease. Now what?

Getting answers to our health concerns isn’t easy. It can take years, many physicians, many dismissals and many misdiagnoses before we end up with an autoimmune diagnosis. 

It took Selma Blair 7 years to receive a Multiple Sclerosis diagnosis.

It took this ballerina 8 doctors before she received a Hashimoto’s diagnosis.

If you are one of the “lucky ones” to actually get a diagnosis, it can feel like validation. Unfortunately, the diagnosis itself doesn’t actually provide any answers. It’s really just the beginning. The next step is to figure out what caused the immune system to over-respond in the first place. 


As a nutritionist who has an autoimmune disease herself AND sees a lot of autoimmunity in her practice, I can admit: this part is easier said than done. And that’s because autoimmunity often has many triggers & root causes.

What is autoimmune disease?

Collectively, autoimmune diseases are one of the most prevalent diseases in the United States, and women are more commonly affected than men. Some experts go as far to say that autoimmunity is THE mechanism for getting sick and dying in the modern world.

 Autoimmunity is the dysfunction of the immune system. As we all know, our immune system protects us from disease, infection, pathogens and other foreign invaders. Sometimes, though, the immune system can get mixed up. It can start to produce antibodies against our own healthy cells, tissues, and organs. Autoimmunity is literally self attack.


What causes this?


Antigen: a toxin or other foreign substance which induces an immune response

Everyone has an antigen load threshold (everyone’s is different based on genetics, detox capacity). If you stay below threshold, you’re generally fine,. But if you exceed your threshold, this leads to autoimmune disease.

Once the gene for autoimmune disease has been turned on, you can’t turn it off. The only thing you can do is try to bring balance to the immune system so it doesn’t over-respond.

But be before we can balance the immune system, we must first remove the antigens and reduce the load. Before we do this? We have to discover what the antigens are!


It might be environmental — chemicals, mold, heavy metals

It might be food trigger, like gluten

It might be stress and dysregulated cortisol/HPA Axis dysregulation

It might be a gut infection, leaky gut/intestinal permeability

It might be viral, like EBV

It might be some other stealth infection, like Lyme or other tick borne illness

It could be a combination of several of these things.


In my opinion as a functional nutritionist, the place to start to asses autoimmunity root cause is through functional lab testing.

They provide a window into the biochemical processes happening inside you. I often describe it as “looking under the hood”. 

You can see which systems are imbalanced or malfunctioning. It provides insight on where to start and what to address first. 

Functional testing is not inexpensive, yet I have found that when paired with a skilled practitioner, they end up saving money (and a lot of time, energy and frustration) in the long run.


Good tests to start with to assess autoimmune triggers


GI test

to look at intestinal permeability, micro biome mapping, infections/overgrowths, digestive capacity, etc. 

(I use GI Map in my private practice)


HPA Axis/adrenal function

(I use DUTCH test in my private practice and in Your Hormone Revival™. This test also looks at circadian rhythm, melatonin, sex hormones and estrogen clearance.)


Organic Acids Test 

Do you have liver detox issues? Glutathione deficiency? Mitochondrial issues? Yeast overgrowth? This test will show you.


Gluten Sensitivity Testing

Vibrant Wellness Wheat Zoomer or

Cyrex Array 3X


SIBO Breath test

While a GI Map stool test can indicate what’s going on at the level of the large intestine & gut microbiome, a SIBO breath test is looking more specifically at the small intestine — and whether or not there is bacterial overgrowth there.

Note: Organic Acids Test can also be suggestive of a SIBO infection.

Other ideas to keep digging:


EBV panel 

(Epstein-Barr Virus can be a trigger)

Great Plains Mycotox test

(looking for mold exposure)


Cyrex Array 10*

(screening multiple food sensitivities)

*I don’t often do food sensitivity testing in my practice — for a number of different reasons — but I do consider Cyrex to be the gold standard for food sensitivity testing.


This is important note about any IgG food sensitivity testing: 


These tests look at  immunoglobulins. In order for these tests to be accurate, you must actually be able to produce immunoglobulins. If you are on steroids or immunosuppressants, or you have a deficiency in immunoglobulins, these tests might be a waste of money for you because you could end up with a false negative. Before doing any IgG food sensitivity test, you should FIRST get a quantitative immunoglobulin test to help evaluate your immune system status and make sure you’re actually producing immunoglobulins (IgG, IgA, IgM). 


Vibrant Wellnes Neural Zoomer

This test looks at your reactivity to neurological antigens, which may have connections to a variety of neurologically related diseases. This can assess the presence and risk of neurological autoimmunity.


The goal in addressing autoimmune disease is to restore balance to the immune system. In order to do that, you have to address immune triggers, or antigens.

So the first step is to discover triggers, then remove the antigen(s) provoking the immune attack + reduce the overall antigen load. And then from there it’s about balancing the immune system.

Part 2 of this post goes into ways to restore balance to the immune system, and what to do when you’re experiencing an autoimmune flare.