Learn The Connection Between Diet, Digestion, and Autoimmune Disease
Autoimmine Disease Digestion

Learn The Connection Between Diet, Digestion, and Autoimmune Disease

Jessica Stephens
Jessica Stephens

Table of Contents

Autoimmune diseases like Celiac, Crohn’s, Lupus, Rheumatoid Arthritis and Hashimoto’s Thyroidosis are on the rise, with the National Institutes for Health (NIH) estimating that 23.5 million American suffer from at least one condition. Since 70-80% of your immune system is in the gut, it makes sense to examine the connection between your digestion and autoimmune diseases.

First, let’s talk about your immune system

Your immune system is a remarkable and complex defense machine whose function is to protect your body from invading microorganisms. Invaders can access your body through many routes, including skin, mucous membranes and body fluids. You were born with an “innate immune system” which responds to all invaders to isolate and destroy them. Sometimes, invaders can escape the innate immune system, and this is when your “acquired immune system” comes to the rescue. The innate immune system alerts your acquired immune system to the presence of an invader, and the acquired immune system then launches a very specific attack against the invader.

What does this have to do with digestion?

When your digestive system is working as it should, food passes through and is contained within the digestive tract, being absorbed, utilized and excreted appropriately. The innate defenses of mucous and hydrochloric acid in your stomach manage bacteria, viruses, and parasites and begins the digestion of your food. Bile and pancreatic enzymes continue the breakdown in the duodenum, then food is absorbed and passed through the remainder of your intestines for excretion.

For many people, though, the hydrochloric acid is not doing the job of protecting and digesting, so larger food particles and pathogens are being passed to portions of the digestive tract that cannot handle them. The lining of the small intestine becomes damaged by the pathogens and particles, and small holes start to form, which these pathogens and particles pass through. What do they meet on the other side of the intestinal wall? Oh, just 70-80% of your immune system!

Ideally, the pathogens that pass through the lining of the intestinal wall get destroyed by the immune system response. But what about those food particles? The immune system correctly recognizes them as foreign and launches a full-out immune attack, resulting in inflammation and allergies.

Autoimmune disorders develop along this same process of digestive dysfunction, but instead of attacking the foreign particles, the immune system incorrectly attacks tissues that have similar protein patterns (called antibody cross-reaction). This response does not happen for everyone, as certain hereditary predispositions and stress triggers are also a part of the auto-immune equation.

First steps to take

If we trace this process back to the beginning, we can see that to address or avoid autoimmune disorders, we must address our digestion!

Start with a nutrient-dense diet of real foods:

  • organic, low-glycemic vegetables pasture-raised, organic meats and eggs
  • healthy fats from pasture-raised, organic animals
  • non-inflammatory oils such as coconut oil, olive oil and palm oils
  • avoid inflammatory foods, such as grains, dairy, nightshades and processed foods
  • eat in a calm state of mind and chew your food thoroughly
  • get plenty of water and rest

I would love to help you make these changes toward a happier gut and a happier life. I work with people in person and online. Let’s connect and see what we can start together!


  • https://www.aarda.org/news-information/statistics/
  • The Paleo Approach by Sarah Ballantyne, PhD