How To Address Autoimmune Conditions

August 22, 2023 9 min read

How To Address Autoimmune Conditions

Disclaimer: This article is purely informational and makes no claims as to treatment or cure from any supplement or program BodyHealth may offer. If you or someone you know has an autoimmune condition, we recommend you see a doctor trained in functional medicine to help you locate the cause of the disease or condition and recommend a solution for it.

This is the third article in the Autoimmune series.

In the last two articles we covered what autoimmunity is and what causes it.

And in this article we’re going to talk about how to address it.

As we know from the first two articles, an autoimmune condition is when our immune system starts seeing our own cells as foreign invaders (harmful bacteria, viruses, fungi, parasites and toxins) and so attacks our cells.

And this occurs, largely, due to compromised digestive tracts, where toxins are coming in and foreign invaders aren’t being killed off, but are allowed to thrive.

After some time of this, the lining of the intestine becomes degraded, allowing these invaders and toxins to be released into our body. Here they land on nerve cells, joints, glands, muscle tissue, etc., and in one way or another corrupt the protein tags on our cells, confusing our immune cells into thinking our own cells need to be destroyed.

This can cause destruction of cells, harm to our nervous system, joints, organs and glands, as well as raising inflammation and cortisol in the body, lowering energy levels, causing brain fog and slowing recovery.

So let’s see what we can do about this.

First, let’s look at the options available.


When we look at treating some kind of condition or illness, we can look at it from two different angles: addressing the symptoms and working to suppress those, or locating the root cause that is creating the condition, and keeping it created on a daily basis, and address that so that it is no longer being continually created.

But that’s an important point. These conditions are not just the result of something that happened in the past and are now there forever. They may have been triggered by something, but they are being made to continue afterwards.

So if we want the condition to be gone, we need to address it’s root cause.

Unfortunately, the solutions being given now only address the symptoms. And they address it in a way that compromises our overall health.

You see, the way we know something is an autoimmune condition is by the specific antibodies (immune cells) our body is producing.

If our body is attacking the cells of our liver, because the proteins on our liver cells have in some way been corrupted, then it’s doing so with very specific immune cells. And these can be measured.

Take Hashimoto’s. When we do a blood test (we do full blood panels as part of our routine at my clinic, Lifeworks Wellness Center) we look for specific antibodies (immune cells) being produced against two of the proteins that are part of the thyroid gland.

When testing for this, “Normal” is under 25. But when someone has Hashimoto’s we’ll find them in the thousands. Production of them is cranked way up.

Well, the solutions being given now, instead of locating the root of the problem and addressing that, are Advil or aspirin to lower inflammation, or steroids, or a whole new class of drugs that suppress the whole immune system.

But, aside from not addressing what's causing the condition so it can be reversed, look at what this does.

Our immune system is responsible for spotting and eradicating foreign invaders, for helping our body recover from illness or injury, and removing toxins. It’s even part of the recovery process in building muscle.

When we suppress our immune system, now we’re much more open to bacterial and viral infection.

Our ability to heal and recover from daily stressors is reduced.

Our energy levels are lower.

We’re at higher risk of cancer, as it’s our immune cells which locate and destroy cancer cells before they get out of hand.

These drugs literally come with warnings that you could die of tuberculosis or cancer because they suppress immune function.

And they’re quite toxic to the body.

Now, sometimes the condition is so bad, life threatening, that someone actually does need to takes these while the root cause is being addressed.

But that’s when it’s life threatening. If we take them when it’s not, then we can create conditions that make things worse than they already are.

So the important thing is finding what is causing this condition so we can reverse it.

If someone has an autoimmune condition, they should first see a doctor of functional medicine who can help determine exactly what they have, what is causing it, and so what to do about it.

But there are key things to be done along with this that will not only greatly help, but are vital.


When someone comes into my practice with Lyme disease, Rheumatoid Arthritis, Hashimoto’s, Fibromyalgia, or any other autoimmune condition, the first thing we do is a full panel of tests: blood tests, hormone tests, antibodies tests, etc.

I need to know if their antibodies are high, what type of antibodies they are.

I need to know what bacterial infections they have, as they will have them.

I need to know what kind of toxins they’ve been exposed to or are currently being exposed to.

I need to know the state of their hormones and digestive system.

It’s a full investigation.

Once I know, then I know what to do, and, depending on what it is (Lyme, Hashimoto’s, Lupus, etc), while there are going to be specific addresses to those conditions, there will also be overall addresses.

This is because, for example, while a tick bite, in the case of Lyme, may have triggered the condition, it was able to take root due to a multitude of factors that were already present and which stayed present.

So here are key things that need to be addressed with anyone who has an autoimmune condition.



First, we need to look at toxic load.

There may have been a heavy exposure (worked on a farm using glyphosate or were exposed to toxic chemicals when very young).

Or there may just be the normal exposure we all get today through our food, air and water. This may not be so bad for someone who grew up in the 60’s or 70’s, before it started getting very bad, but for someone who was born in the late 80’s, 90’s or after, it can be quite bad and could trigger an early autoimmune condition.

So look for any toxic exposure in your environment and remove this:

  • Get a reverse-osmosis water filter for your drinking water.
  • Eat only organic, grass-fed meats and organic fruits and vegetables.
  • Check for mold in your house or apartment and, if it’s there, get it remedied.
  • Get off alcohol (this is not good for someone with an autoimmune condition).
  • If you work somewhere that exposes you to toxins, if your condition is bad, you’re going to need to find another place to work. If you don’t, the condition will not clear up.
  • Look for any toxic chemicals in your cleaning supplies at home, toiletries, deodorants, skin care products. The majority of those on the market today have some very toxic ingredients. Go to to find non-toxic alternatives.
  • And, of course, you will need to do a detox to remove toxins from your body. This is necessary, but it will be a little bit later on as we need to address our gut first to ensure real detoxing can occur. Right now we just want to stop new toxins from entering.


Next we need to address the gut. We’ll have harmful bacteria in the small intestine (SIBO), and possibly in the stomach as well. We will very possibly have several different types of bacteria and possibly parasites and a fungal overgrowth (candida). All of these contribute to this condition and worsen it by degrading the lining of our gut.

There are several things to do here to address this:

First, get off any processed sugars. These feed the harmful bacteria, viruses, parasites and fungi, and any treatment of these will fail if we continue consuming what feeds them.

Also lower sugar levels in general. You will want to go onto a paleo-type diet for this.

At the same time, you will need to raise protein levels as this are necessary for repair and many people with autoimmune conditions are quite protein-deficient.

We need to address digestion. If digestion is weak, as it will be in this case, this is letting these harmful bacteria through so they can do their damage.

This means no acid neutralizers of acid blockers as these lower the amount of acid in your stomach, thus allowing foreign invaders through.

It also means no soda drinks or carbonated waters as these neutralize stomach acid as well.

Next is, with the help of your functional medicine doctor, addressing the harmful bacteria, parasites and fungi that are present and removing these from your system.

And then there is repairing the damage done to the intestinal lining which is now letting foreign invaders and toxins through, into your blood stream.

For this we need to do a Leaky Gut protocol to help repair the lining. Until it’s repaired these things can still get through.

Then we need to address the colon, where our microbiome (beneficial bacteria) is. These bacteria are vital for overall health and our immune system, and the above toxins and foreign invaders cause havoc here.

This is a lot, I know, however, if you’re interested in a full gut protocol that addresses this, our Gut Health Challenge and guide is coming in the next two weeks. 

And I’ll be taking you through all of this, both with in-depth information and exact steps.


Last is diet. This is both to ensure we’re getting the nutrition our bodies need to heal and operate, but also to ensure we’re not consuming things that are furthering our condition.

Lectins, as found in certain foods, can act in the same way on the lining of our intestine as harmful bacteria and toxins do. They can also in some cases act as a poison and can raise inflammation. Look for a list of foods high in lectins and remove these from your diet.

While many people have no trouble with gluten (found in grains such as wheat, rye and barley), more and more people today do, possibly due to it's association with glyphosate for the last 5 decades. Gluten contains two proteins (gliadin and glutenin) that act to degrade the intestinal wall, contributing to Leaky Gut, and these should be removed from your diet.

Food sensitivities are another big one and will be different for everyone. While these should be properly tested for, you may already know some foods you are sensitive to. When we have a food sensitivity it can act as an autoimmune trigger, creating an immune response against it. Any foods you are sensitive to should be removed from your diet.

Make sure you’re getting plenty of high quality protein and fats — absolutely no trans fats.

This means staying away from processed foods which can contain adulterated fats that are harmful to our cells, and which are also very high in omega 6 fatty acids, which raise inflammation levels.


Alright. I know that was a lot. But when we have an autoimmune condition we really do need to do all of the above.

Our body and our immune system is being overwhelmed. With every item we remove, we lower the amount of things that are triggering the autoimmune condition and keeping it going, and it can lessen.

Unfortunately, most individuals who have an autoimmune condition already had a compromised immune system to begin with. So while the above may seem overboard, it truly is needed to actually address and reverse the condition.

Beyond the above there will be other things that need to be addressed, which your functional medicine doctor will go over with you.

If there are hormonal deficiencies caused by the condition, but which are themselves furthering the overall problem, then hormone therapy may be needed until the condition is reversed.

With various autoimmune diseases there can be different, specific bacteria causing harm.

For instance, with Lyme we actually have several bacteria that came in with the original tick bite and some can take some time to fully kill off and have exact remedies.

When we look at reversing an autoimmune condition, we’re really trying to handle each one of these factors that are stimulating the condition and keeping it created.

We have specific antibodies (immune cells) that attack different parts of the body and these can be measured.

But as we address each of the above things, taking away that which is triggering the condition, these antibodies, which are the main things causing inflammation, start to decrease.

We can start seeing improvement in the first 2 months, or possibly 4 if the condition is very bad, and a full reversal in 6 to 9 months or possibly a year.

It takes time with this one and requires discipline and a real lifestyle change. But it can be done. We do it every day at my clinic.

And it's very much worth it for the life you get back.

So I hope this helps some. We do have, right around the corner, our Gut Health Guide and 30-Day Challenge. This is a very in-depth guide that jumps into every aspect of our gut and how to raise our gut health to optimal levels.

And, right after that, as gut health must be addressed first, we have our Detox Guide and challenge.

I think you’ll enjoy them and I hope to see you there!

*These statements have not been evaluated by the Food and Drug Administration. These products are not intended to diagnose, treat, cure, or prevent any disease.