The Root Causes of Diarrhea

The Root Causes of Diarrhea
While diarrhea can be caused by a variety of reasons, it’s important to know what is at the root of it in order to resolve your symptoms.

Are there times when you find yourself running to the bathroom every chance you get? While diarrhea can be caused by a variety of underlying things, it’s important to know what is at the root of it in order to resolve your symptoms. Because diarrhea is definitely not a pleasant thing to experience!

But first – what is diarrhea? Sometimes occurring alongside nausea, vomiting, or even abdominal pain, diarrhea is loose, watery, and frequent bowel movements. If caused by a food borne illness, it usually only lasts several days, but if you can’t seem to get rid of it, it’s time to look deeper to find out what’s really going on.

What Causes Diarrhea?

Food Allergies

When you have a true food allergy, there is an immediate immune response to something you eat. For example, if you eat something you’re allergic to, the symptom occurs right away, such as stomach pain, intestinal cramping and/or diarrhea. Of course other symptoms like swelling of the mouth and throat and/or hives can occur if the allergy is severe. 

Food Sensitivities

Food sensitivities, on the other hand, are a bit different from food allergies. With a sensitivity, the body’s reaction to the food can take up to three days to occur. In some cases, even longer. This makes finding out your food sensitivities challenging at times, as symptoms may change day to day based on what you ate the days prior. But just like food allergies, food sensitivities can cause diarrhea so it’s important to find out what foods your body doesn’t tolerate well. Food sensitivities can also cause just about any symptom in the body to occur also, such as joint pain, rashes, brain fog etc… Learn more about the differences between food allergies and sensitivities here.

Food Intolerances

Food intolerance is another reaction your body can have to food. A common intolerance is lactose intolerance. Lactose is a milk sugar found in milk and dairy products. For a person with lactose intolerance, their body has a deficiency of the digestive enzyme required to break down lactose, leading to bloating, gas, cramping, and even diarrhea.  There are several other examples of food intolerances that cause symptoms such histamines, oxalates, salicylates and more.

Food Poisoning

Food poisoning occurs after eating food contaminated with a microorganism, such as bacteria, viruses, parasites or toxin-like chemicals, that result in GI upset, mainly nausea, vomiting and diarrhea. If you’re exposed to any pathogenic bacteria, this can become a cause of diarrhea. One such bacteria, E.Coli, can be a problem when you drink contaminated food or water – often during times of travel. This diarrhea is commonly called traveler’s diarrhea.  Other food borne causes of diarrhea in the U.S. include staph aureus, salmonella, shigella, campylobacter, yersinia, giardia, norovirus and clostridium perfringens.  The duration of symptoms after eating or drinking contaminated food can range from a few hours to several days after ingestion depending on the pathogen, and your body’s immune system response to it. 

Bacterial and Yeast Overgrowths and Chronic Low Level Parasitic Infections

It is also possible that an overgrowth or imbalance is caused by bacteria and/or yeast that are normally part of your gut microbiome, but become out of balance and create symptoms.  C.diff is a perfect example of that, as it is commonly caused by prescription antibiotic treatment that can cause anywhere from mild to severe and life threatening diarrhea. In addition, when at infectious levels, it is also contagious. Other examples include candida (or other yeast) that can overgrow after a course of antibiotics or after other changes occur in the gut microbiome.  It is also possible to have low levels of parasites such as giardia, blastocystis, entamoeba, and even different types of worms that may be the cause of diarrhea.  This is why it is important to get a comprehensive stool analysis to determine what the root cause may be. 


Small intestinal bacterial overgrowth or SIBO is when the bacteria levels in your small intestine grow to levels that aren’t normal for your body, and overproduce hydrogen gasses (hydrogen and/or hydrogen sulfide) . This causes symptoms like diarrhea, gas, bloating, or even fatigue, brain fog, and rashes. Many times, SIBO occurs with nutrient deficiencies as well, since the small intestines’ job is to absorb nutrients from the food you eat. SIBO can also occur after an episode of food poisoning or course of antibiotics, so it is important to keep SIBO in mind since it can be a root cause of diarrhea in those 2 common instances. 

Autoimmune Disease of the Gut

Sometimes autoimmune diseases of the gut are the source of diarrhea. Things like celiac disease, Crohn’s disease, and ulcerative colitis are autoimmune in origin. However, in functional medicine we will still be looking at what the root causes/triggers are that contributed to the autoimmune disease starting.  Since over 80% of the immune system is in the gut, diarrhea can be a common symptom in gastrointestinal autoimmune disease. It’s important to follow up with your provider if your diarrhea lasts longer than several days and you’re having difficulty finding ways to improve the symptoms. 

Motility Disorders

Motility disorders of the gastrointestinal system impact how slow or fast food contents move through your intestines. In motility disorders, the digestive system has lost the ability to coordinate muscle movement from the esophagus all the way down to the anus. This can cause bloating, cramping, diarrhea, constipation, and even abdominal pain. If it’s a rapid movement disorder, the contents in the digestive system move too quickly, leading to loose and watery stools, and thus may be part of the root cause of diarrhea. 


During times of stress, your body responds by going into “fight or flight” mode. While this reaction helped us evolve as humans in life or death situations – like running away from a lion – sometimes the fight or flight response is less helpful in modern times. Digestive changes occur during the fight or flight response, which can lead to symptoms of a “nervous stomach” such as intestinal cramping and diarrhea.  Adopting a daily relaxation practice such as meditation or deep breathing can be really helpful, as well as adding on extra sessions during times of high stress and/or before a stress event such as public speaking. 


Did you know that taking too many or the wrong forms of certain supplements can be a root cause of diarrhea? While magnesium is an amazing and important mineral, too much magnesium can cause loose stools.  The most common form that causes this is magnesium oxide as it is poorly absorbed by the GI tract, however even too much of well absorbed forms like magnesium citrate can also contribute. Make sure you do your research on which supplement to take based on your needs when you start a magnesium supplement. Generally magnesium glycinate is the supplement we recommend, as it is well tolerated by the GI tract. Here’s a great one to start with.

While magnesium is just one supplement that can cause diarrhea if taken incorrectly, there are others that can cause similar issues if taken incorrectly. Aloe is one such supplement and has a natural laxative effect, so too much can result in diarrhea or abdominal cramping. However, aloe can be a great addition to a regimen to help treat constipation. 

Another one to be aware of is betaine HCL. This is a great supplement for those with low stomach acid, but make sure to consult with your provider on the correct dosage, as taking it incorrectly can lead to diarrhea as well as other GI symptoms. Lastly, bile salts can also lead to diarrhea as taking too much pulls water into the intestine, causing watery stools. Ultimately, make sure to do your research and consult a provider before taking one of these supplements to make sure they are actually needed. 

Even probiotics that can be incredibly helpful and gut healing can be the root cause of diarrhea and other GI symptoms if it is not the right blend for you!  See my previous blog on the different types of probiotics and their benefits for more information. 

Wow – quite the list, right? But getting to the root cause of your diarrhea doesn’t have to be hard – that’s why working with a functional medicine provider can help pinpoint the problem sooner so you can get back to living life without those nagging GI symptoms. 

Effective Ways To Manage Diarrhea Symptoms

  1. Manage your stress. Integrate yoga, meditation, or exercise into your daily routine. Stress management can help reduce your risk for autoimmune disease and diarrhea!
  2. Try doing a simple food elimination. The food categories that cause the most problems include gluten, dairy, sugar and highly processed/packed foods. Try doing an elimination diet for 30 days then reintegrating these foods into your diet to see if any symptoms arise.  Not sure how to do this?  I built an entire program around it to help guide you. 
  3. Stay hydrated. Since you’re losing more fluid with loose stools, give your body what it needs by drinking enough water.

Support Your Gut Health With Functional Medicine!

Here at Arizona Wellness Medicine, we have a team of highly trained functional medicine providers to create a personalized plan for you so you can feel your best. We want to get to the root cause of your diarrhea so you can get back to feeling your best. Schedule an appointment here.



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