Diarrhea can take control of your life. I’m not talking about the average tummy bug kind of diarrhea. I’m talking about the type of diarrhea that lasts for days, weeks, months, or even years…chronic diarrhea. 

Diarrhea can disrupt the rhythm of your daily life, and take a real toll on your body. But, the good news is that you do not have to live with chronic diarrhea! Diarrhea is a treatable medical condition. Together, we can uncover what’s causing your diarrhea, help to treat your symptoms, and get you back on the road to good health. 


Diarrhea Symptoms

Passing loose, watery stools three or more times per day is the primary symptom of diarrhea. Other symptoms can accompany diarrhea including:

  • Belly bloating
  • Cramping
  • An urgent need to use the bathroom
  • Nausea
  • Abdominal pain 

Some people can experience more severe symptoms including:

  • Blood or mucus in your stools
  • Fever or chills
  • Vomiting
  • Light-headedness or dizziness 


What Causes Diarrhea?

There are a variety of factors that can cause diarrhea. Temporary diarrhea, lasting one to two days, can result from a viral infection, the food you ate or traveling. 

On the other hand, chronic diarrhea can indicate a more serious problem. The most common causes of chronic diarrhea include inflammatory bowel disease (Crohn’s disease and ulcerative colitis), chronic infections, and malabsorption syndromes (cystic fibrosis, Celiac disease, lactose intolerance, etc.)  in which food is not digested and absorbed. 

Chronic diarrhea is a common complaint amongst our patients. Below are seven of the most common causes of chronic diarrhea that we treat including gallbladder removal, IBD, gut dysbiosis or pathogen imbalance, histamine intolerance, gluten intolerance or Celiac, dairy intolerance, and SIBO. 


1. Gallstone or surgical removal of the gallbladder

Frequent loose, watery stools after having gallstones or having your gallbladder removed (cholecystectomy) is common. The gallbladder collects bile to release when you eat aiding in the digestion of fats. Removing the gallbladder takes away the main storage site for your bile acid. Instead, the bile acid is stored in the gut causing it to be less concentrated and drain into the intestines. Once in the intestines, it can have a laxative effect making stools looser. 

GI transit times can also be altered after gallbladder surgery causing transit times to decrease in the small intestine and accelerate in the colon. This impairs the body’s ability to absorb water from your stool leading to looser, watery stools. 

2. IBD

Inflammatory bowel diseases (IBD), including Crohn’s, Ulcerative Colitis, and other types of colitis (microscopic or lymphocytic colitis), are diseases of chronic inflammation. IBD causes tissue destruction and inflammation of the bowel walls limiting the body’s ability to absorb fluids. This results in loose, watery, or even completely liquid stools. 

Patients with IBD may experience frequent and urgent bowel movements because fluid moves more rapidly through the intestine. You may also see blood in or on the stool and experience extreme weight loss, anemia, fever, and loss of appetite.

3. Gut Dysbiosis or Pathogen Imbalance 

Gut dysbiosis is a generic term for an imbalance in gut flora. Our digestive tract contains a delicate balance of different kinds of bacteria. When one species becomes overgrown or gets wiped out, the balance is thrown off leading to diarrhea along with many other symptoms. 

There are several pathogens known to cause gut dysbiosis including bacterial, yeast, parasites, and viral pathogens.

  • Acute Bacterial Pathogens: The most common bacterial organisms to cause diarrhea include: e coli, shigella, Campylobacter Jejuni, Citrobacter, yersinia enterocolitica, salmonella, and Staphylococcus aureus. Chronic bacterial toxins like those secreted by C Difficile can also lead to diarrhea. Older adults in healthcare facilities, like hospitals or nursing homes, or who have recently been on antibiotics, are more at risk for contracting C Difficile.
  • Yeast and Fungal Overgrowth: Rapid growth of Candida (a yeast) and cryptococcus (a yeast-like fungus) in the GI tract can lead to diarrhea, especially after antibiotic use.
  • Parasites: Intestinal parasites including giardia, entamoeba histolytica, Cryptosporidium Parvum, and Protozoan parasites like blastocystis hominis, Cyclospora, Dientamoeba Fragilis, Entamoeba coli, and endolimax nana can cause diarrhea. Parasitic infections are often, but not always, marked by stomach cramps, bloating, nausea, and watery diarrhea. 

4. Histamine Intolerance

Histamine is a chemical that notifies the brain when to release stomach acid for digestion. And, it is part of our response to injury or an allergic reaction. Histamine intolerance occurs when the body is unable to break down enough of it in the intestines, causing histamine levels in the blood to rise. 

Histamine intolerance can result from a multitude of factors including a combination of genetics, and a leaky gut. This leads to decreased secretion of DAO enzyme (used to break down histamine), liver detox overburden, and dysbiosis. 

5. Gluten Intolerance or Celiac 

Gluten, a protein found in wheat, can cause inflammation in the gut and can change the structure of the gut wall. For people with gluten intolerance or Celiac disease, gluten can cause chronic diarrhea along with other GI symptoms. 

6. Dairy

Dairy products contain three components that can cause diarrhea: lactose, whey, and casein. 

Lactose intolerance is an inability to digest lactase, a sugar found in milk products. Lactose intolerance occurs when the small intestine does not make enough of the digestive enzyme lactase. This condition is common in adults with a genetic predisposition or after an injury, disease, or infection of the small intestine. Lactose intolerance causes diarrhea by increasing the volume of water in the colon, which in turn increases the volume and liquid content of the stool.

Casein and whey, the two proteins in milk products, can cause an allergic reaction when the body thinks the protein is harmful. Most people with an allergy to casein or whey have symptoms that appear as infants and outgrow them with age. However, patients with gut wall damage can experience dairy protein intolerance with diarrhea and other GI symptoms. 


SIBO is an overgrowth of bacteria in the small intestine. Normally, the small intestine contains fewer bacteria than the large intestine and is focused on food absorption. For many who have SIBO, diarrhea is a common symptom.  

How is Chronic Diarrhea Diagnosed

The key to diagnosing chronic diarrhea is to uncover the underlying root causes so that we can address them and prevent future relapses. Common tests for patients with chronic diarrhea may include:

  • Comprehensive Stool Microbiome Testing – A stool sample can be used to evaluate the root cause of digestive tract issues. Functional medicine stool tests provide information about absorption, digestion, yeast overgrowth, bacterial imbalance, parasite infection, inflammation, metabolic activity, and immune function.
  • SIBO Breath Testing with both lactulose and fructose for best accuracy 
  • Blood Test – Specific blood tests can help identify celiac disease antibodies and yeast antibodies. 
  • Imaging – Imaging can include endoscopy, colonoscopy, or sigmoidoscopy and is generally used to diagnose or rule out Inflammatory Bowel Disease or structural issues as a driver for symptoms.  


Natural Remedies and Treatments for Diarrhea

The challenging part of treating diarrhea is that there is not a one size fits all treatment plan. Many mild cases of diarrhea will resolve on their own. But, for more severe, chronic cases of diarrhea there are a variety of natural remedies and treatments available.


Specific Carbohydrate Diet (SCD):

The SCD diet is incredibly effective at stopping urgent, frequent bowel movements. This is for you if you run to the bathroom 10 to 20 times per day. The SCD diet focuses on removing carbohydrates that are not fully digested and remain in the gut leading to an overgrowth of harmful bacteria.  It is particularly helpful for my patients who have Crohn’s disease, celiac, ulcerative colitis, and chronic diarrhea.

Download a free guide to properly starting the SCD diet from the team at Healthy Gut.

Starch and Meat Diet:

A starch and meat diet is an alternative to the SCD diet that works for some people. This whole-food diet is focused on eating foods like white rice, white potatoes, meat, fish, and poultry. Like the SCD diet, this diet limits all processed and canned foods. 

Diet Considerations During Flare-Ups:

Curing the cause of chronic diarrhea can take time. And, flare-ups happen. During diarrhea flare-ups keep these diet considerations in mind.

  • Be cautious with fruit, except for bananas
  • Raw vegetables can be hard to digest and cause GI upset
  • High amounts of fats and oils can be difficult for a sensitive digestive system. Limit high-fat foods like egg yolks, cream, oils, and bacon.

Many other diets (low FODMAP, Low Histamine, Low Salicylate, Low Oxalate, or Autoimmune Paleo) can be useful for the treatment of diarrhea depending on the underlying causes.


Stress Reduction

Have you ever had to run to the bathroom before a presentation or a big event? That’s your gut responding to stress! Increased levels of stress can cause changes to your gut motility, which means that your body can slow down or speed up food processing based on your levels of stress. 

Active stress relief activities are a critical component of naturally treating diarrhea. Try watching a funny movie, taking an Epsom salt bath, meditating, or practicing moderate exercise daily.  



Many of your body’s metabolic processes occur during the night, including digestion. And, sleep provides your body the much-needed energy for digestion to happen.

A few nights of poor sleep might not have a major impact on your GI health. But, chronic insomnia or poor sleep can impact your GI and contribute to your chronic diarrhea.



Depending on the cause of your diarrhea, a variety of supplements may be beneficial to you. I often incorporate the following supplements into my patient’s treatment plans. 

Digestive Enzymes:

After eating, enzymes break down the food so that we can absorb the carbohydrates, fats, and proteins. Without enzymes, larger food pieces remain in our gut and begin to ferment, feeding the bacteria. This can either slow down digestion or speed it way up. 

There has been significant research indicating the successful use of digestive enzymes to support patients with chronic diarrhea. The key to digestive enzymes is taking enough with the right balance of acidity for them to work. It may take some time, but my patients who use digestive enzymes report amazing results!

I recommend Holozyme by Healthy Gut.

High Dose Probiotics:

High-dose probiotics have been shown to balance the gut microbiome and improve intestinal permeability promoting intestinal barrier functions and alleviating many inflammatory responses.

Depending on the cause of your diarrhea, I recommend a variety of probiotics usually containing 250 (or more) organisms daily to help control diarrhea. Below are a few of my go-to probiotics:

  • S. Boulardii, a probiotic yeast strain, is my number 1 go-to for helping alleviate diarrhea, especially if it was a result of antibiotic use. But, in my clinical experience, patients with IBD should proceed with caution with introducing S. boulardii because Anti-Saccharomyces cerevisiae antibodies (ASCA) have been associated with Crohn’s disease. Saccharomyces Cerevisiae (Brewer’s/Bakers yeast) is similar enough to S Boulardii that the immune systems of sensitive individuals can cross-react, potentially triggering a symptom flare.
  • Bacillus Claussi, a spore-forming probiotic, is an effective probiotic for treating diarrhea, preventing antibiotic associated diarrhea, and may be viable as the only treatment in some cases of SIBO where tolerated.
  • Bacillus Subtilis is a multifunctional probiotic ideal for preventing the growth of bacteria and enhancing nutrient digestion. HU58, a strain of bacillus subtilis, is used for the management of antibiotic-associated diarrhea in adults.
  • Lactobacillus Rhamnosus GG (LGG) is one of the most widely used probiotic strains and it is ideal for patients with histamine driving their diarrhea. In addition, there are many well-documented studies showing that LGG is indicated for the prevention and treatment of gastro-intestinal infections and diarrhea.
  • UltraFlora Intensive contains Lactobacillus plantarum 299v, a probiotic strain of lactic acid bacteria that is naturally occurring in the human gut. This probiotic is excellent at decreasing anti-inflammatory symptoms making it ideal for reducing diarrhea in patients with IBS, C. diff, spontaneous colitis, and high E coli levels. 
  • High-dose lactobacillus, found in TheraLac, promotes healthy, rapid growth of all beneficial bacteria that can boost immune health and promote regularity. 

Immunoglobulins or Colostrum:

Immunoglobulins and colostrum help strengthen the body’s natural immune system. While also fighting bacteria and viruses that cause diarrhea. I recommend utilizing a bovine-derived serum that is lactose-free to repair and support healthy gut barrier functions.

Chinese Herbal Formulas:

This is far from an exhaustive list of Chinese herbal formulas for diarrhea, but these are three of my favorites to use with my patients. 

  • Shen Ling Bai Zhu San – Usee for poor nutrient absorption, bloating, and/or loose stools.
  • Raise Qi – Helpful for poor digestion, bloating and gas pain, chronic diarrhea, and loose stools.
  • Huo Xiang Zheng Qi San – Ideal for treatment of acute diarrhea or travelers’ diarrhea.   


Short-Term Support in a Pinch

When you’re in a pinch, it’s always helpful to keep a few diarrhea treatments in your arsenal. I recommend keeping these on hand: 

  • Bismuth Subsalicylate: Also known as Pepto-Bismol, increases the amount of fluid your intestines can absorb while reducing inflammation and overactivity of your intestines. Note that both liquid and chewable Pepto-Bismol may contain fermentable sweeteners. Follow the label for dosage.
  • Imodium: Imodium works to slow motility for sudden diarrhea. Follow the label for dosage.


I Can Help Identify the Cause of Your Diarrhea and Get You Back on the Path to Good Health

Are you ready to troubleshoot your chronic diarrhea? Get a better understanding of your digestive health and the natural approach to resolving diarrhea once and for all, by booking a free 15-minute call with me. 

If after the call you come on board as a patient, your clinician will order the best tests for your specific situation, and develop a unique treatment plan so that you can get back on the road to good health.



 “Symptoms & Causes of Diarrhea | NIDDK.” https://www.niddk.nih.gov/health-information/digestive-diseases/diarrhea/symptoms-causes. Accessed 31 Mar. 2022.

 “GI-MAP® Interpretive Guide – Diagnostic Solutions Laboratory.” https://www.diagnosticsolutionslab.com/sites/default/files/u16/GI-MAP-Interpretive-Guide.pdf. Accessed 6 Apr. 2022.

“Histamine: The Stuff Allergies are Made of – MedlinePlus.” 1 Apr. 2019, https://medlineplus.gov/medlineplus-videos/histamine-the-stuff-allergies-are-made-of/. Accessed 6 Apr. 2022.

“Enzyme therapy for functional bowel disease-like post-prandial ….” https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6910206/. Accessed 12 Apr. 2022.

“Probiotics for infectious diarrhea – PMC – NCBI.” https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1773578/. Accessed 19 Apr. 2022.

“Bacillus clausii – The Probiotic of Choice in the Treatment of Diarrhoea.” https://www.longdom.org/open-access/bacillus-clausii–the-probiotic-of-choice-in-the-treatment-of-diarrhoea-2157-7595-1000211.pdf. Accessed 12 Apr. 2022.

 “Bacillus subtilis HU58 and Bacillus coagulans SC208 Probiotics ….” 11 Jul. 2020, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7409217/. Accessed 12 Apr. 2022.

“Towards a better understanding of Lactobacillus rhamnosus GG – PMC.” 29 Aug. 2014, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155824/. Accessed 12 Apr. 2022.

The role of Lactobacillus plantarum 299v in supporting treatment of ….” 25 Jan. 2021, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7882405/. Accessed 12 Apr. 2022.