12 Common Causes of Diarrhea Most People Don’t Know


Being stuck on the toilet with diarrhea sucks. I’ve spent a significant amount of time there. However, I’m lucky compared to my friend Jordan who had years of steady, chronic diarrhea.

The worst part of this is we aren’t alone. There are millions of people just like us who experience occasional diarrhea or even daily bouts. And sadly, it’s the world’s 2nd leading cause of death in children.

The silver lining to this unfortunate problem is that diarrhea is solvable. It’s completely fixable and not something you have to live with if you don’t want to. One of these twelve causes of diarrhea could be a stand-alone problem for you, but oftentimes the case will be more complex with several of them contributing to your daily bathroom habits. The key is that you are willing to dive deeper than modern medicine typically goes and use an engineering mindset to solve this issue. (More on this at the bottom of the post.)

You’ll notice that Irritable Bowel Syndrome (IBS) isn’t on this list. That’s because IBS in and of itself is not a cause of diarrhea, but the issues below are part of why your doctor might have told you you have IBS.

Our goal here is to give you a hit list that you could actually print out and take with you to your next doctor’s appointment. From here, you can have an educated discussion about troubleshooting your chronic diarrhea. This list is based on functional medicine and years of helping people struggling with this complex issue.  

Gut Dysbiosis

Gut dysbiosis is a catch-all term for an imbalanced gut flora. Various well-known experts refer to it differently, as there is currently no single accepted definition of the location or the exact issue with the gut flora that this term refers to. That being said, in our digestive tract there is a delicate balance between different kinds of bacteria. If a certain species overgrows or gets wiped out, the balance can be thrown way off. Also, the whole colony of bacteria can be too small or too large and this can cause issues. One of the many possible results of this is diarrhea and sometimes persistent diarrhea. It’s very important to maintain a diverse gut flora that is at the right size (not too big or small).

Recommended Next Step:  If you think gut dysbiosis is an issue for you, changes will be coming. But first your next step is to get a better understanding of just how bad your digestive health is – start with this gut health quiz.

SIBO – Small Intestinal Bacterial Overgrowth

The majority of the 100 trillion bacteria that are in our digestive tracts are located in the large intestine. The small intestine contains much much fewer. It is designed to be the location for food absorption. It’s not designed to harbor a lot of bacteria, but in many people who have diarrhea this can be the reason. SIBO is an overgrowth of bacteria in the the small intestine and for many who have this condition, diarrhea is the result (others have constipation). SIBO is a type of gut dysbiosis, but the difference is that there are tests and a known location of the dysbiosis.

Recommended Next Step:  SIBO is a much bigger deal than people are aware of. Dr. Allison Siebecker is one of the world’s leading researchers and doctors to see if you have it. Listen to her explain it on this SIBO podcast.


Parasites feed off their hosts, causing harm and commonly diarrhea. It’s a major myth that people in developed areas of the world don’t get parasites. They are much more common than most people realize. Humans can pick up parasites from pets, contaminated water, food and contact with other human waste. Common parasites that cause diarrhea are Giardia, Strongyloides, Entamoeba histolytica and Cryptosporidium. It’s been our experience that a large percentage of people who have chronic diarrhea have a parasite.

Recommended Next Step:  The world of parasites is complex and confusing so start with learning about these 10 very common ones that we’ve seen.

Yeast Overgrowth

Candida is the most common yeast that overgrows, but any overgrowth of yeast is not good for gut health. Yeast is a fungus that is a normal part of human gut flora colonies. In healthy amounts, it actually aids in digestion and keeps us healthy. But when too much yeast is present it can start to damage the gut lining. Excess yeast can release harmful toxins that start to affect the gut wall and your bowel movements causing gas, bloating, and diarrhea.

Recommended Next Step:  Don’t fall prey to the anti-candida diet. I think there are many problems with it and several alternatives. Watch this short video.

Gluten (and Wheat in General)

Let’s be honest, gluten and wheat taste delicious. But unfortunately they might be causing you diarrhea. Gluten is a problematic protein found in wheat and has been shown to have toxic effects in our guts. It causes inflammation in the gut and can alter the structure of the gut wall leading to symptoms like diarrhea. Some people are less tolerant of gluten than others. If you have a gluten intolerance or Celiac disease it could be the culprit of your GI distress. An important point is, as the research becomes clearer, we are learning that wheat and other grains contain many other compounds beyond gluten that could cause diarrhea.

Recommended Next Step: If you’re curious about how gluten, gliadin and other parts of wheat interact with the digestive tract and cause damage read this in-depth article.

Dairy, Oh Sweet Dairy

Dairy has three components that can be common causes of diarrhea: lactose, whey and casein. Lactose intolerance happens to some people as they age. They lose the enzyme needed to break down lactose. When this happens the lactose can’t be used by the body and ends up feeding bacteria instead, which typically leads to diarrhea. Casein and whey are the two proteins in milk that can cause diarrhea for those with gut wall damage. Dairy protein intolerance is often mistaken for lactose intolerance and therefore it’s wise to cut all dairy out for a period of time if you are experiencing diarrhea.

Recommended Next Step: Truth is, not everyone needs to be dairy-free and many people like me can remove it, feel better and then re-introduce it later without issues. Here’s a short video on that process.

FODMAPs (Fermentable Oligosaccharides, Disaccharides, Monosaccharides And Polyols)

As gut health breaks down, almost any food can cause problems. But FODMAPs are especially problematic for those with damage. FODMAPs are a group of sugars/carbohydrates that depending on the health of your gut and some genetic factors can cause diarrhea. These undigested bits of food have an ability to draw extra fluids into the gut, through a process called osmosis (a fancy term for how water moves). All the extra build up of stuff in the gut is a cue for water to rush in creating a watery mixture that the body must get rid of ASAP. In our opinion, people who are sensitive to FODMAPs typically have other underlying issues that caused the FODMAP intolerance. As the other issues are resolved, the ability to digest FODMAP foods typically comes back.

Recommended Next Step: The FODMAP diet isn’t always what it appears. While it can significantly help diarrhea, not eating FODMAPs can cause health issues later on. I explain why in this article.

Emotional Stress

Did you know your gut is actually programmed to respond to stress? Have you ever been really nervous before an important event like a first date, public speaking event or competition event and had to run to the bathroom? If so, you’ve felt this phenomenon. The gut is home to the Enteric Nervous System. It’s like your 2nd brain, but only it contains way more neurotransmitters than your brain.

Anything that can excite that wonderful network of neurons in your gut can cause increased motility. Motility in your gut comes from a wave-like movement called peristalsis. This wave-like movement is controlled by special cells that generate the wave and are affected by nervous system signals. Stress has different effects on the different parts of your GI system. It  increases motility in the colon while simultaneously decreasing motility in the small intestine. This slowdown of food processing in the small intestine may lead to SIBO and damage to the mucous lining of the gut. If you are currently under constant emotional stress due to “life happening” this could be part of why you are having diarrhea.

Recommended Next Step:  Read this article on 3 easy steps for managing stress and helping improve digestion.

Physical Stress

Working out is great for health. But if you are overdoing it, you could be damaging your gut. When we work out, a lot of heat builds up in the tissues of your intestines. This can lead to inflammation and irritation of the gut. For your gut the worst kind of exercise is long duration, medium to high intensity, like long distance running for marathons and triathlons.

There is also an effect where blood that was directed away from your GI system during workouts rushes back in afterward and can potentially cause further gut damage.

Both of these are physical stresses that can cause diarrhea. What’s clear is that exercise is generally more beneficial than harmful. However, part of the reason why you’re having diarrhea could be due to your exercise habits.

Recommended Next Step:  If you’re going to beat your body up in athletic events and hard exercise at least take recovery serious and enjoy weekly epic epsom salt baths.

Inflammatory Bowel Diseases (IBD)

The two main inflammatory bowel diseases are Crohn’s and Ulcerative Colitis. As the name suggests these are diseases of chronic inflammation, which creates the conditions in the intestines for diarrhea. Food may pass through the bowels too fast or slow as a result of inflamed areas of the gut. Our experience also tells us that people with IBD typically have underlying reasons for the inflammation, which are things like infections, hormone imbalances and/or food intolerances.

Recommended Next Step:  Getting an IBD diagnosis isn’t the end of the world and we’ve seen and helped many people get amazing recoveries. This article answers most people’s first question, which is how long will it take.

Fat Malabsorption

Fat is necessary and vital for health. It is the building block of all hormones in the body. But some people, due to a variety of factors, end up in a position where their bodies can’t break down and absorb fat that is eaten and when this happens diarrhea follows. The reason isn’t always straightforward but it can be related to damage to the intestinal tract, gall bladder issues like pancreatic insufficiency and bile acid problems. The great thing is as you heal the other issues contributing to diarrhea, this problem typically resolves itself as well. But in the meantime to stop the diarrhea try paying attention to dietary fat absorption.

Recommended Next Step:  If you end up decreasing your fat intake, it’s common to eat too little calories and end up being malnourished. Until you fix this issue you’ll need to make some changes to your diet. Check out the fat malabsorption weight gainer shake I created here.

Traveler’s Diarrhea

Maybe it was Montezuma’s revenge, or perhaps it was that street cart you ate from in India, or maybe it was just that produce you bought fresh from the village market but didn’t quite wash enough. Anyway you slice it, Traveler’s Diarrhea is not fun. You may be thinking, “Yeah, I had it,  but that couldn’t be what’s causing my diarrhea now.” You may have overcome the virus or bacteria that caused the onset of diarrhea, but this isn’t the end of the story. Recent research is showing that just one experience with Traveler’s Diarrhea can significantly change your gut flora and a percentage of people end up developing SIBO and/or gut dysbiosis after such extreme infections. If you’ve ever gotten sick while traveling, it may be related to your current cause of diarrhea, especially if you used antibiotics to get rid of the infection.

Recommended Next Step:  The best thing you can do is lie low, see your doctor and try these at-home flare recovery steps.

Unravelling the Mystery of What Causes Your Diarrhea?

Even after two years into following the Specific Carbohydrate Diet, every 6 weeks or so Jordan would have a nasty couple days locked in the bathroom. People on the internet and uninformed medical professionals blamed cheating, cross-contamination and supplements for his issues.

However, when he got stool tests back that showed a gut infection of Strongyloides, well it was pretty clear what his issue was. A round of antiparasitic treatment and his seemingly “random” bouts of diarrhea were gone.

The reality is diarrhea seems undeniably complex when first learning about it. And that’s because it’s typically a combination of the factors mentioned above, as we’ve learned studying this for the past 6 years.

It varies from person to person. Jordan and I were different, and so are the 1000’s of people we’ve talked and worked with.

Once you get comfortable with the fact that there’s no one-size-fits-all prescription for people with diarrhea, then you begin to realize it’s actually easier than it’s ever been to fix it and reverse any damage it’s been doing to your body.

If this is a problem for you, even if it’s an occasional problem, I can guarantee you a few things:

  1. Diarrhea will strike when you least like it to (like dates and parties)
  2. It’s a reliable marker that your health is not anywhere as strong as you’d like to believe
  3. It’s fixable and if the right actions are taken you can trust your stomach again

The body is a system of systems. It’s the perfect engineering problem and that’s why using engineering principles of solving problems work so well to fix health issues. Start with the next steps above and then be prepared if you want to fix this once and for all to explore advanced testing, trying dietary tweaks and supplements.

We explain all this and more in our Stopping Diarrhea presentation.

Check out our Stopping Diarrhea presentation here.

This is the year for action. This event is designed to give you our proven diarrhea action steps to stop it, find out the causes and fix them. You can have control again; the information in this presentation will empower you to do that.

Grab your access to Stopping Diarrhea here.


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