Runner’s Stomach – What it is and how to avoid it

Female runner bent over with stomach pain

You may have heard this term in runner or triathlete circles and wondered what it is.  Or maybe you’ve heard it referred to as “runner’s trots” or “runner’s diarrhea”.  Regardless of what you call it, there’s no way to make it sound pleasant.  I’m pretty sure, though, that if you’ve had it, you know exactly what I’m talking about. 

If you’re a runner or triathlete, it’s a safe bet you’re no stranger to talking about poop.  It’s a very common issue, with studies showing between 30-70% of athletes reporting some sort of gastrointestinal (GI) distress with exercise. (2

Unfortunately, I’m well acquainted with this issue. I’ve had IBS for years, but thought I had it under control…until I started distance running. For my first full marathon, I made the mistake of eating something new on race morning and ended up stopping no less than 10 times at the port-a-potties during the race. I vowed right then to never let that happen again!

Even if you’ve personally never experienced runner’s stomach, if you’re tackling a new distance or adding in more intense workouts, you have a greater chance of developing issues as you ramp up duration and intensity.  So, let’s dive in, shall we?

What is Runner’s Stomach?

Runner’s stomach is digestive distress in the lower GI tract that is brought on by exercise.  It can present as bloating, gas, cramps, the urge to have a bowel movement, and/or diarrhea.  Sometimes upper GI distress, including nausea and vomiting, can be present as well.

What Causes Runner’s Stomach?

There are multiple factors that can contribute to runner’s stomach.  While underlying conditions such as irritable bowel disease may be an issue for some athletes, other athletes can be afflicted as well.  Here, I’ll focus on the factors that cause GI issues in athletes without underlying GI conditions. We can break these factors down into 4 main categories: physiological, mechanical, environmental, and nutritional.

Flowchart of common causes of gastrointestinal issues when exercising.


Physiological factors relate to adaptations that occur naturally within your body in response to exercise.

As soon as you start exercising, your body begins redirecting blood flow from your GI tract to those tissues that are critical for exercise, such as muscles, lungs and cardiovascular tissues. (3)  Blood flow to the GI tract decreases by up to 80% during strenuous exercise.  The extent of the decrease in blood flow is impacted by exercise intensity and duration, hydration levels, and heat stress. (2)

Reduced blood flow leads to a cascade of effects that can cause stomach issues for some athletes.  These effects include slowed movement of food through the GI tract and damage to the intestinal wall, which can then lead to reduced absorption of fluids and nutrients, toxins leaking through the intestinal wall, and inflammation. (2)

As noted, exercise intensity and duration impact how much blood is redirected from the GI tract.  Studies have shown that athletes who participate in ultra-endurance events report higher incidence of GI symptoms compared to those who do shorter distances, including even marathon distance. (2)

Athletes who do more than one training session in a day tend to have more frequent episodes of GI distress as well.  It takes the intestines about 4-5 days to repair when injury is present, so researchers suspect that inadequate recovery time between training sessions is at least partly to blame for increases in GI symptoms for athletes with such rigorous training schedules. (2)

It should be noted that exercise is a form of stress for the body.  Stress hormones and the gut microbiota mutually influence each other.  This relationship is another probable factor contributing to GI issues during exercise. (2)


Mechanical factors are those that are related to the physical movements involved in doing the activity.  Specifically, running involves bouncing from one foot to the other repeatedly.  This bouncing can jostle the contents of your stomach and bowels and is believed to contribute to GI issues while running. (2)

While runners are not the only endurance athletes who tend to have GI issues, from the mechanical perspective runners are more likely to have lower GI symptoms like cramps, gas, and diarrhea.  Cyclists tend to have more upper GI concerns like nausea and reflux due to cycling in the bent-over position.  Swimmers also tend to have more upper GI issues due to gulping air. (2


The temperature in which you are exercising plays a significant role in GI function. (1) Water losses through sweat and increased body heat when exercising in hot conditions cause decreased blood volume throughout the body, further decreasing blood flow to the GI tract.  Less blood flow leads to more damage to the tissues in the intestinal wall, allowing more toxins to pass through. (2)


While digestive issues during exercise often have nothing to do with nutrition, some athletes are sensitive to certain dietary practices.  Specifically, excessive intake of carbohydrates, as well as timing of fiber, fat, and protein tend to impact GI function during exercise. (2) Another common cause of GI issues in endurance sports is inadequate hydration. (1)

High carbohydrate intake can cause GI distress in athletes who are not accustomed to consuming large amounts of carbs.  Just like your muscles and cardiovascular system, your gut needs to build up to endurance-level carb intake through training.

Additionally, high fructose intake often leads to digestive issues.  The absorption rate for fructose is limited and high intake can lead to incomplete absorption.  Your body absorbs other types of sugars via different pathways from fructose.  Carbohydrate foods or supplements that contain a combination of different types of sugars are often better tolerated for this reason. (2)

Another group of carbs that have gained attention as GI irritants in endurance athletes are FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides and polyols).  These are small sugars that are not easily absorbed by the body and often cause digestive issues, including gas, bloating, cramps and diarrhea and/or constipation.  I will dive deeper into this in a future post, but it deserves mention as FODMAP sensitivity is fairly common. (2)     

Fiber, fat, and protein slow down digestion.  While all of these nutrients are important to a healthy diet,  timing of intake is key.  Since exercise already slows movement in the GI tract, anything that remains in your gut when you’re running will just get jostled around and potentially cause issues. (2

Special Considerations for Women

Studies have shown that women have slower transit times in the stomach and in the large intestine.  Women also have less colonic muscle contractions to push food along the GI tract. (3)  This means that it takes us longer to clear food from our systems, which is important to note for timing pre-workout/race fuel.

In addition to the physiological differences in the digestive system between women and men, female hormones also influence the gut.  During the luteal phase of the menstrual cycle (time period between ovulation and menstruation), the transit times in the intestines may be even slower due to high progesterone levels. (3)

Chart showing the phases of menstrual cycle and fluctuations of estrogen and progesterone throughout.

Research has also revealed a bi-directional relationship between sex hormones, including estrogen and progesterone, and the gut microbiome.  This means that not only do your hormones impact the types and quantities of gut bacteria, but the bacteria are also believed to play a role in hormone production. (3)

 It’s no wonder female recreational marathoners report higher rates of GI symptoms than their male counterparts! (3)

Tips for Minimizing Runner’s Stomach

You may have read this and gotten the impression that endurance training is bad for gut health.   That couldn’t be further from the truth!  While long and/or intense exercise does create some challenges for the gut and potential digestive issues, the rewards far outweigh the risks and there are some adjustments you can make to your routine to minimize symptoms.

Hydrate, hydrate, hydrate!  Make sure you have a plan and take in sufficient fluids before, during, and after exercise.  Include electrolytes as needed.  Aim for loss of less than 2% of your body weight during an exercise session. (2)   

Adjust amounts and timing of fiber, protein, and fat intake prior to exercise until you find what works for you.  During training, you should be practicing your fueling strategy, so this is the time to play around with it.

Gradually increase carbohydrate intake over the course of training.  Your gut is adaptable, so if you are unable to tolerate adequate amounts to support your level of training, build up slowly until you reach levels that optimize endurance and performance.  Choose carbs that have a mix of different types of sugars for improved tolerance. (2)

During long workouts, frequent and consistent intake of carbohydrates is believed to help protect your gut from damage. (2) Note that a lot of sports supplements contain high levels of fructose, so read those labels.  If opting for whole foods to fuel your workout, choose low fat, fiber, and protein foods such as blueberries or medjool dates.

If you don’t have time before your workout to allow for sufficient digestion, formulated liquid sports products may be easier on your stomach.


While endurance athletes may have special conditions that can make them more prone to digestive issues, including the dreaded runner’s stomach, there are steps that you can take to keep you running to the finish line, not the porta-potties!

First and foremost, always have a good hydration plan that takes into consideration weather to avoid under-hydrating.

Second, avoid fueling before and during workouts with high-fructose foods or supplements.  Opt for foods that have a mix of different types of sugars.  Less than 50% of the sugar should come from fructose.

Pay attention to timing of pre-workout fuel.  If you are consuming something within a few hours of your workout, opt for foods that aren’t high in protein, fat, or fiber.

Additionally, if you’re training for an event, use your training to find the right fueling plan.  Your gut can be trained, so build up your carb load over multiple training sessions and play around with different fuel sources and timing until you find what works for you.

When in doubt, a dietitian that specializes in sports can help.  If you’re interested in learning more about working with me, send me a message to schedule a free informational call! I can work with you to put together a comprehensive diet and fueling plan to fit your goals, uncover any potential food sensitivities, and determine optimal timing of nutrition for training and for race day.

I also have a FREE guide with great ideas for pre-workout snacks that are easily digested. Click here to download The Busy, Active Woman’s Guide to Pre-Workout Fueling On-the-Go!

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