Today we’re covering the top 7 causes of leaky gut, aka intestinal permeability. Just keep in mind there are more, for sure, but as a clinician that treats digestive health almost exclusively in the busy Byron Herbalist clinic these are the conditions that stand out to me as strong and obvious causes.
The gut lining or the intestinal epithelium is a single layer of cells that acts as a barrier between the digestive tract and the rest of the body. It’s really quite amazing how many different functions it provides including playing a role in nutrient and water absorption, modulating the immune system and even microbial defence.
When you look at the gut wall in a broader sense it’s easy to see how damage and disruption to this lining could play a role in allergies, inflammation, digestive symptoms, nutrient deficiencies and even autoimmunity.
But what drives leaky gut? Let’s dive into the top 7 causes that I see in the clinic now!
SIBO as a driver of leaky gut
Sometimes in the clinic I feel like all I talk about is SIBO and it’s not just because it’s a condition I am fascinated by but more because I strongly suspect that many patients I work with have this bacterial overgrowth in their small bowel. Along with many other consequences SIBO is a strong driver of gut damage leading to leaky gut.
How would a bacterial overgrowth in the small bowel lead to gut damage and permeability? It seems pretty straight forward and obvious but always good to see researchers teasing out the details. One study from the Scandinavian Journal of Gastroenterology looked at the connection between SIBO and leaky gut. The researchers outlined how the two drivers below could lead to the gut damage.
- Direct bacterial injury to the gut wall
- Immune system activation leading to an inflammatory response
I see SIBO patients all the time in the clinic. Sometimes this can be a tricky condition to treat and often people are looking for answers they are struggling to find. Often I will look to resolve the bacterial overgrowth first and from there I will look to heal and seal the gut lining. This isn’t always the best approach and if a patient is dealing with strong allergic and histamine symptoms like headaches, blocked nose, itchy skin and tissue swelling or strong food intolerances then sometimes working on healing the gut lining and lowering the inflammatory load on the gut can really help before going after the overgrowth!
When treating SIBO often I will look to resolve the bacterial overgrowth first and from there I will look to heal and seal the gut lining.
Candida and Leaky Gut
A close second is candida overgrowths. This fungal imbalance can wreak havoc on the digestive tract and when significantly overgrown can drive gut damage and leaky gut too.
The process is more technical than you would think but to keep it simple Candida can adhere to the gut lining in our digestive tract, morph from a unicellular yeast to a hyphal formation and then form biofilms. The more virulent strains of Candida are much more adept at starting this whole process (2).
Whether it’s SIBO, SIFO, or large bowel imbalances, if you suspect you have leaky gut, DO NOT neglect microbiome imbalances as a major driver.
Whether it’s SIBO, SIFO or large bowel imbalances from Candida or bacterial if you suspect you have leaky gut DO NOT neglect microbiome imbalances as a major driver!

Coeliac disease and Leaky Gut
This is a simple one. Along with many autoimmune diseases coeliac disease – ie the autoimmune version of a gluten allergy – is synonymous with leaky gut. In fact this is one of the ways you can get a diagnosis for coeliac disease. A gastroenterologist can perform an endoscopy and look for flattened villi which are finger-like projections from the gut wall.
Beyond coeliac disease, researchers are looking more and more into the link between leaky gut and a broader range of autoimmune diseases with decent evidence pointing to leaky gut as a driver of autoimmunity (3).
When I first came across the extensive research connecting leaky gut to autoimmunity I started testing most of my autoimmune patients. Most of them did have leaky gut, some of them didn’t and only a few of them improved when the only thing we did was focus on healing the gut lining. As with all complex and chronic diseases leaky gut is only part of the problem with most autoimmune cases.
IBD and Leaky Gut
Now this is a tricky one. Is it inflammatory bowel disease that is causing leaky gut or is it leaky gut that is causing inflammatory bowel disease. Different cases will have different angles here but one thing is for sure, leaky gut is almost a given with most active IBD cases!
We could spend an entire article worth on the science exploring leaky gut and IBD and this is something I focus on intently when working with most of my IBD patients. For best insight and targeted approaches I firmly recommend extensive stool testing to give us an insight into drivers of this condition which typically include
With the above drivers in play and a genetic predisposition to run with inflammation it’s easy to see how inflammatory bowel disease can flare.

Toxic Exposure and Leaky Gut
Whether we’re talking about environmental toxins like heavy metals, pesticides, or other industrial chemicals or biotoxins like mould derived mycotoxins, toxic exposure is a huge driver of leaky gut. Let’s start from the simple side and move to the more complex in a minute. If your body is under toxic load, your detox enzymes will be working overtime, these enzymes use different nutrients (minerals and vitamins) which will become depleted over time. Many of these nutrients help to build and maintain the gut lining. Zinc is a great example here (5).
If we take mould illness for example we can see that certain mycotoxins like trichothecenes produced by stachybotrys and fusarium can cause necrotic lesions on the GI tract, shorten the villi height leading to malabsorption and increase leaky gut (6). It would be too simple to explain the extreme allergic presentation of most mould affected people by pointing to leaky gut but as with most complex illnesses there is way more going on here including mast cell activation, inflammation and tissue damage too.
Clinically I find mould to be a major driver of gut dysfunction. Not to be ignored or minimised if you’re chronically unwell! See more here on common binders I would recommend to treat mould exposure.
Nutrient deficiencies and Leaky Gut
Zinc, vitamin A, vitamin D, amino acids and more all work together to build and repair the gut lining. There are many reasons that you might be nutrient deficient from the simple answer – not eating a nutrient dense diet – to issues around maldigestion or malabsorption – you’re eating a high quality nutrient dense diet but it isn’t getting broken down and assimilated properly.
There have been a few stumper cases I’ve worked on where we’ve found leaky gut, treated the overgrowths and went on quite a persistent and involved gut lining healing approach with minimal improvements. Finally finding chronically low levels of zinc and vitamin D helped to improve the leaky gut issues.
Some research has found that leaky gut co-presents with patients who are critically ill. The researchers found a connection between low levels of vitamin D and early developments of leaky gut (7).
Drug induced Leaky Gut
There are a few pharmaceuticals that are strongly linked to leaky gut. This should actually be at the top of this list as they are probably the most common causes of leaky gut in certain populations. The top of the top are a class of drugs called non-steroidal anti-inflammatories or NSAIDs. These can commonly be purchased over the counter and people turn to them to manage pain – ibuprofen or aspirin are NSAIDs you may have heard of or even taken before. The other class of medications that can cause leaky gut are cancer fighting drugs including chemotherapy.
‘Virtually all studies agree that all conventional NSAIDs increase intestinal permeability in the human within 24 h of ingestion and that this is equally evident when they are taken long term.’
Summary: Top 7 Causes of Leaky Gut
So there you have it, 7 of the top causes of leaky gut that I see in the clinic. If you relate to any of these common drivers of leaky gut and are looking for digestive health support you can find a spot to book in below!
References and Resources
- Small intestinal bacterial overgrowth and intestinal permeability
- Disruption of the intestinal mucosal barrier in Candida albicans infections
- Increased Intestinal Permeability: An Avenue for the Development of Autoimmune Disease?
- All disease begins in the (leaky) gut: role of zonulin-mediated gut permeability in the pathogenesis of some chronic inflammatory diseases
- Zinc and gut microbiota in health and gastrointestinal disease under the COVID‐19 suggestion
- Mycotoxin: Its Impact on Gut Health and Microbiota
- Association of Intestinal Permeability with Admission Vitamin D Deficiency in Patients who are Critically Ill
- Intestinal permeability in the pathogenesis of NSAID-induced enteropathye

1 comment
Great breakdown of the main causes of leaky gut! It’s surprising how many everyday habits can impact gut lining without us realizing it.