Many of my clients are familiar with the phrase “autoimmune begins in the gut”, however, most are not sure what it means. Today, I would like to unpack this issue in more detail. 

Firstly, it is important to start with the fact that autoimmune disease is on the rise in our society. According to the National Institutes of Health, 8% of the U.S. population is living with an autoimmune disease, and 80% of those with an autoimmune disease are women. The category of autoimmune diseases includes more than 140 diseases that can affect every organ in the body and can occur at any point across the lifespan. 

You might know someone who has an autoimmune diagnosis like Hashimoto’s Thyroiditis, an autoimmune disorder where the immune system mistakenly attacks the thyroid gland. Multiple Sclerosis or MS is another common autoimmune disorder that attacks the central nervous system, specifically the brain and spinal cord, leading to a variety of symptoms like fatigue, vision problems, numbness and tingling, muscle weakness and spasms, cognitive changes, and balance and coordination issues.

This is no laughing matter! The immune system is attacking itself. 

As a functional nutritionist, I do not diagnose or treat any disease process, however, I have worked with hundreds of clients with an autoimmune diagnosis. Together we focus on a whole food, anti-inflammatory diet, and a test do not guess approach. The goal is to assess and address root causes of inflammation in the body by getting key data provided by gut and food sensitivity testing. 

Why would I start with gut health? So, your gut is not just about digesting food, it is a major hub for your immune system. In fact, about 70-80% of your immune cells are in and around your gut, in what is called the gut-associated lymphoid tissue (GALT). This means your gut is constantly interacting with your immune system, deciding what is safe (like nutrients from food) and what is a threat (like harmful bacteria or viruses).

Now, imagine your gut lining as a protective wall with tiny gates that let in only the good stuff, like nutrients, while keeping out harmful invaders like bacteria and viruses. However, if that wall becomes damaged—say, from stress, poor diet, infections, or even medications—it can develop tiny cracks. This is what we call “leaky gut” or intestinal permeability. When this happens, undigested food particles, toxins, and bacteria can slip through those cracks and enter your bloodstream. Your immune system sees these as foreign invaders and launches an attack.

Over time, if this process continues unchecked, your immune system can become overactive and confused. It may start attacking your own tissues by mistake, which is the hallmark of autoimmune disease. We say autoimmune begins in the gut—because a damaged gut lining can set off the chain reaction that leads to immune dysfunction.

The good news? By healing the gut, we can often calm the immune system and stop this cycle. This involves identifying and removing triggers (like inflammatory foods or infections), repairing the gut lining with nutrients like L-glutamine and zinc carnosine, and restoring balance to the gut microbiome with probiotics and prebiotics.

Supporting digestive function is also foundational when addressing gut health and its connection to autoimmunity. From a functional perspective, digestion is the body’s highest healing priority because it is the starting point for everything else. If we are not properly breaking down and absorbing nutrients, the entire system suffers.

Here’s how poor digestive function ties into gut health and autoimmunity: 

• Low Stomach Acid (Hypochlorhydria): Without adequate stomach acid, proteins are not broken down properly, leading to larger food particles entering the small intestine which can irritate the gut lining and contribute to leaky gut. Low stomach acid also impairs the absorption of key nutrients like B12, zinc, and magnesium—nutrients critical for immune regulation.
• Enzyme Insufficiency: Pancreatic enzymes are essential for breaking down fats, proteins, and carbohydrates. If these enzymes are insufficient (often due to stress, poor diet, or low stomach acid), undigested food particles can further damage the gut lining and feed pathogenic bacteria, worsening dysbiosis which is a predominance of bad versus beneficial bacteria in our microbiome.
• Bile Flow: Proper bile flow is necessary for fat digestion and detoxification. Biliary stasis (poor bile flow) can lead to fat malabsorption, which not only affects nutrient absorption but also contributes to inflammation and gut dysfunction. Bile is also necessary for the process of peristalsis, the movement of food and toxins through the gut. So poor gallbladder function can contribute to constipation, poor motility, and a backed-up detoxification system where toxins are recirculated back to the liver versus being escorted out of the body and into the toilet. 
• North-to-South Process: Functional digestion works like a domino effect, starting in the brain with the sight and smell of food and moving downward. If one step is disrupted like eating too quickly in stress mode, it creates a cascade of dysfunction further down the line. This is why I always emphasize supporting the entire digestive process, from top to bottom.

Of course, there is so much more to unpack on this subject, however, this should give you an idea of how gut health and autoimmunity are related. Also, it is much easier to address autoimmune via functional nutrition in the preliminary stages of a diagnosis. However, it can be a powerful approach at any stage of a diagnosis to help rebalance and strengthen the system and reduce overall body wide inflammation. 

Certainly, this is also a plug for prevention. If you are having gut issues, my advice is do not wait or hesitate and let years go by without getting to the root of what is going on, and unfortunately this is a scenario I see on a weekly basis. 

And as always, I am happy to chat more. Below is the link to book a free, 20-minute phone consultation to talk more about your concerns. I would love to help.