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Breaking Down the Link Between Leaky Gut and Autoimmunity

Does leaky gut cause autoimmunity?

  • What is autoimmunity?

  • Understanding the concept of a “leaky gut”

  • Does leaky gut cause autoimmune diseases?

  • How to heal a leaky gut?

  • The signs-leaky gut is healing

  • Takeaway

  • FAQs

Gut health and autoimmunity

We trust our “gut feelings” the most, don’t we? It’s odd to think that this term isn’t just an expression but has a rock-solid scientific justification. The 2000-year-old Hippocratic adage, “It all starts in the gut,” still holds true. Science says that an unhealthy gut, otherwise called a leaky gut and autoimmune diseases are closely linked . Does leaky gut cause autoimmune diseases? Yes! From poor immunity, weight gain, and hormonal imbalances to something as simple as a headache, everything is influenced by the health of your gut (2). In this blog, we shall explore why and how to cure leaky gut to cure autoimmune diseases.

What is autoimmunity?

Autoimmunity, or autoimmune diseases, occurs when your body's immune system mistakenly targets your healthy cells and tissues as toxic foreign particles. This can be assaulting to your body's tissues. Your body’s immune cells, like lymphocytes, macrophages, eosinophils, etc., initiate severe inflammation in various organs and body parts, causing poor health conditions. 

Multiple sclerosis (MS), rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), or lupus, and ankylosing spondylitis are examples of some common autoimmune diseases.

Understanding the concept of a “leaky gut”

The gut encompasses your stomach and the intestines. Every time we eat, drink, or expose our body to foreign chemicals, we are either nourishing our gut or potentially feeding it with disease-causing agents. This determines the quality of your general health.

Does leaky gut cause autoimmunity?

The Gut - the Origin of Immunity

While the food is being digested and absorbed, the gut's unique "mucosal barrier"—a thick, solid wall of cells with tight connections—keeps unwanted foreign particles from passing into the body. As a result, the first sign of an immune response (essentially a protective reaction) begins in the gut. The gut microbiota also contributes to this immunity.

cure leaky gut cure autoimmunity

The gut houses trillions of microbes collectively called the “microbiota.” A significant portion of the gut microbiota aids in digestion. These microbes break down the fiber we consume, help maintain health by producing vitamins and other vital nutrients and regulate the gut-immune system (3). Thus called the “friendly microbes.”

Similar to any ecosystem in nature, the gut contains harmful pathogens as well. These pathogens modify digestion to produce toxins rather than nutrients. Candida overgrowth, intestinal parasites, and small intestine bacterial overgrowth (SIBO) are the most prevalent conditions due to bad microbiota in the gut (4). 

The secret to a healthy body is to keep the good and bad microbes in balance

The Gut - a War Zone.

Gut is the battlefield between good and bad microbiota. When you abuse your gut with junk food, sugar, nightshades, alcohol, GMOs, a sedentary lifestyle, drug abuse, and stress, the number of pathogenic microbes grow exponentially. This leads to "dysbiosis,” or the harmful microbes outnumbering the good ones (5). When the toxins from the harmful microbes overflow, they can sometimes leak through the tight tissue barrier of the gut into the blood. This is called a "leaky gut."

If the gut wall is healthy, leakages won’t happen as the intestinal wall has multiple layers of protection. These layers are designed for self-repair. However, if the gut walls are abused persistently, like in the case of infections, medications, food intolerances and stress, the tight junctions between the cells in the gut wall become loose. This makes the gut wall permeable leading to leakage.

How to heal a leaky gut

Your gut wall is designed to guard you against by-products of food digestion, toxins, endotoxins, microbes, and partially digested food particles, but now when you have a leaky gut, all these are sneaking past the drawbridge and into your bloodstream.

As a result, the immune system reacts to those parts of your body that receive a flow of these toxins or foreign bodies, leading to a leaky gut linked to autoimmune disease.

Does Leaky Gut Cause Autoimmune Diseases?

As soon as your gut becomes leaky and toxins, viruses, bacteria, and food particles start to flood your bloodstream, your immune system recognizes these invaders as dangerous and initiates inflammation to get rid of them. If untreated, your immune system releases waves of inflammation, and more and more particles get into your blood circulation. It eventually becomes stressed out, works less efficiently, and targets your body cells. This causes a leaky gut linked to autoimmune disease (6).

Does leaky gut cause autoimmune diseases - the Hidden Concept

Some of this leaked sludge from the gut resembles human body cells. This process of mistaken identity is called “molecular mimicry.” This confuses your immunity, and they attack your own cells, assuming them to be foreign. 

The best example would be autoimmune thyroid diseases like Hashimoto's and Grave’s disease. These are often caused by the molecular mimicry of gluten and dairy products.

The target organ of an autoimmune disease defines it. Rheumatoid arthritis can develop if toxins affect the joints; Hashimoto's or Grave's disease can result if it affects the thyroid gland; and Crohn's or colitis can appear if it affects the gut lining.

How to heal a leaky gut?

While there is no one-size-fits-all approach to healing a leaky gut, there are several strategies that may be helpful. In the past ten years, there has been an increase in the use of probiotics and prebiotics to treat leaky gut. We at Functional Medicine Clinic are here to guide you through this journey to cure leaky gut to cure autoimmune diseases.

The six-step approach to healing the gut is:

  • REMOVE IRRITANTS The objective is to eliminate or remove elements that harm your gut, such as foods that cause allergies, bloating, discomfort, infections, and known stomach irritants. Inflammatory foods like gluten, dairy, maize, soy, eggs, and refined sugar should be completely eliminated. Maintain a food journal to observe other foods that may be triggers & eliminate them.

  • RESTORE NUTRIENTS Attempt to restore the missing components of your gut, thereby restoring its health. Replenish all nutrients that were lost due to dietary changes, medications (such as antacids), illnesses, or ageing. These nutrients are necessary for normal digestion and absorption using bile acids, stomach acids,  digestive enzymes and nutrient deficiencies.

  • REPAIR THE LEAKS It's crucial to provide the gut with the nutrition it needs to heal itself. In this process, protein is essential. Amino acids, literally "seal the leaks" or perforations in your gut by repairing damaged cells and aidin g tissue regeneration.  L-glutamine is another vital amino acid that helps revitalize the gut wall lining and is one of our favorites.

  • REMOVE PATHOGENS Test and treat for h pylori, parasites, fungus (candida), and other dysbiosis.

  • REINOCULATE HEALTHY MICROBES Add an extra dose of good bacteria to balance the gut microbiome. It is important to not add random probiotics to your regime. Probiotics with right strains of helpful bacteria should be chosen.

  • RETAIN HEALTH You must maintain that healthy gut environment with diet, vitamins, minerals, protein and lifestyle changes. 

The Signs to Show That the Leaky Gut is Healing

Apart from poor gut health, environmental factors also play an important role in  autoimmune diseases. Your general health and the signs of autoimmune illnesses improve as your leaky gut recovers. 

It may take some time to fully recover from a leaky gut, but there are various indications that the process is moving in the right direction:

Signs that the leaky gut is healing

  • Better Digestion Digestion may improve, with fewer signs like bloating, gas, and constipation, as the gut lining gets stronger and healthier.

  • Decreased Disease-Specific Symptoms The joint pains of RA, stomach pains and bloating in Crohn's disease, and sore skin conditions in lupus are some of the many signs and symptoms that slowly reduce in the healing process. 

  • Less Fatigue & Brain fog An increase in energy levels may result from improved nutrition absorption when the gut is in good health. This leads to fewer episodes of weakness and fatigue. Brain fog will start clearing up. 

  • Glowing Skin It might result in brighter, healthier-looking skin since the gut is better equipped to get rid of the toxins.

  • Better Immunity The immune system may operate better as the gut lining is stronger, resulting in fewer episodes of infection and better overall health.


The classic concept of autoimmune diseases being caused by the genetic makeup of a person or from contact with environmental triggers has been challenged by adding a third component: the leaky gut. Science has clearly explained how a leaky gut causes autoimmune diseases (7). We at The Functional Medicine Clinic strive to empower our patients with knowledge about  leaky gut linked to autoimmune disease and help recover from it. It is never too late to start the journey to a healthy gut. If you or your loved ones show signs and symptoms of autoimmune diseases, do not refrain from using our holistic approach that helps to cure leaky gut to cure autoimmune diseases.

Book a free discovery call with our Functional Medicine Doctor to start your recovery.


  1. What is the fastest way to heal a leaky gut? Although there isn't a quick remedy for a leaky gut, a variety of tactics, such as avoiding trigger foods, maintaining a nutritious diet, controlling stress, and taking the right supplements, might encourage gut repair.

  2. How long does it take to repair a leaky gut? The time it takes to repair a leaky gut varies depending on the individual's condition and the approach taken. It can take weeks to months to see a significant improvement, and ongoing maintenance is often necessary.

  3. How can I heal my gut naturally? Try removing trigger foods, eating a balanced diet, controlling stress, taking probiotics (under guidance only), supplementing with gut-healing nutrients (under guidance only), addressing infections and limiting exposure to toxins if you want to heal your gut naturally.


  1. Mu Q, Kirby J, Reilly CM, Luo XM. Leaky Gut As a Danger Signal for Autoimmune Diseases. Front Immunol. 2017 May 23;8:598.

  2. Paray BA, Albeshr MF, Jan AT, Rather IA. Leaky Gut and Autoimmunity: An Intricate Balance in Individuals Health and the Diseased State. Int J Mol Sci. 2020 Dec 21;21(24):9770.,paves%20the%20way%20to%20autoimmunity.

  3. Mangalam AK, Yadav M, Yadav R. The emerging world of microbiome in autoimmune disorders: Opportunities and challenges. Indian journal of rheumatology. 2021 Mar;16(1):57.

  4. Paray BA, Albeshr MF, Jan AT, Rather IA. Leaky gut and autoimmunity: an intricate balance in individuals health and the diseased state. International journal of molecular sciences. 2020 Dec 21;21(24):9770.

  5. Yaigoub H, Fath N, Tirichen H, Wu C, Li R, Li Y. Bidirectional crosstalk between dysbiotic gut microbiota and systemic lupus erythematosus: What is new in therapeutic approaches?. Clinical Immunology. 2022 Sep 8:109109.

  6. Mu Q, Kirby J, Reilly CM, Luo XM. Leaky Gut As a Danger Signal for Autoimmune Diseases. Front Immunol. 2017 May 23;8:598.

  7. Zhang Y, Peng Y, Xia X. Autoimmune diseases and gut microbiota: a bibliometric and visual analysis from 2004 to 2022. Clinical and Experimental Medicine. 2023 Mar 1:1-5.


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