GI Issues in Endurance Sports: A Troubleshooting Guide for Athletes
- 3 days ago
- 8 min read
Updated: 1 day ago
Is there anything more frustrating than dealing with stomach pain, runner's trots, nausea, or other pesky GI issues while training or racing? It’s a challenge that many endurance athletes (and especially distance runners) face, even if they don’t talk about it.
If this is something you struggle with, you're in the right place. In episode 137 of The Eat for Endurance Podcast, I'm joined by Sports Dietitian Kylee VanHorn, RDN for a deep dive conversation all about GI issues in endurance athletes.
Kylee and I discuss:
Why GI issues are so common during endurance exercise
Different causes of upper and lower GI symptoms
Why you may need to stop blaming the gels
How hydration and sodium intake influence GI tolerance
Common fueling mistakes that contribute to stomach issues
The role of underfueling and low energy availability
How to train your gut for higher carb intake
Fueling strategies for marathons, triathlons, and ultras
Why GI troubleshooting is often more complicated than athletes expect
When GI symptoms may warrant further medical testing
GI issues in endurance sports are very common, but they’re not something you just have to accept as “normal.” With the right fueling strategy, hydration plan, and a bit of troubleshooting (all of which a sports dietitian can help you with), you can significantly improve if not completely eliminate your symptoms.
Why Do Endurance Athletes Get Stomach Problems?
During exercise, blood flow is diverted away from the gut and toward the working muscles, meaning digestion is not being prioritized. Running jostles your stomach, which further increases risk of GI trouble if you're not careful about what you consume. Also, the longer you exercise, the more time there is for things to go sideways.
As Kylee explained during the episode, athletes often want to blame their GI problems on their gels or sports drink:
“People come into the work under the assumption that it has to be the gels… or this drink mix… or the carbs. Oftentimes, I find that it is not the actual gel itself that is causing the issue.”
Of course, there are situations where a specific product or mixture of products truly doesn’t work for someone, and a quick switch improves their symptoms.
But more often than not, GI issues stem from a combination of factors:
Low energy availability: Chronic underfueling can slow down GI function and worsen stomach problems during exercise, even if things seem fine in daily life.
Dehydration and sodium imbalances: Both too little and too much sodium can contribute to symptoms like a sloshy stomach, nausea, and cramping. Getting your fluid and electrolyte intake dialed in is often the first place to start when troubleshooting.
Hyper-concentrated drink mixes: Putting too many scoops in your bottle, or stacking a concentrated drink mix with a gel and not enough water, can overwhelm your gut and draw fluid into the intestine, leading to diarrhea, gas, and cramping.
Inadequate gut training: Taking in more carbs than your gut is trained to handle is a common culprit, especially for athletes ramping up their fueling for longer races.
Heat and altitude: Both increase intestinal permeability and raise your fluid and electrolyte needs, making symptoms more likely if your plan isn't adjusted accordingly.
Underlying GI conditions: Things like H. pylori, gut microbiome imbalances, or other GI conditions can fly under the radar in daily life but show up clearly during exercise. This is one reason why persistent symptoms are worth investigating further.
This is also why troubleshooting GI issues can take time. There usually isn’t a single “magic fix,” and what works for one athlete likely will not work for another.
I see athletes all the time trying supplement after supplement, or cutting out food groups (gluten, dairy etc) trying to get to the bottom of their GI issues. While I get why they're doing this, it's not the right approach. It can even make the problem worse, as restricting foods frequently leads to underfueling!
How to Train Your Gut to Prevent GI Issues
Another major takeaway from this episode is that gut training matters, like… really matters.
Just like your muscles and cardiovascular system adapt to training, your gut adapts too.
Gradually practicing your race fueling strategy during training helps your digestive system better tolerate fluids and carbohydrates during longer or harder efforts.
This process takes time, consistency, and patience. Everything must be practiced prior to race day, and can't be rushed. Like Kylee said, “There are no shortcuts to gut training.”
I always work with my clients to identify their nutrition targets as well as where they're currently at, and we slowly work up to their fueling goals over many weeks, if not months.
That means practicing with:
Fluids
Sodium
Gels, chews, or other carb-containing sports products
Solid foods (some with protein/fat), if needed
You also need to practice fueling in different environmental conditions (e.g. heat, altitude etc), and at different intensities, depending on what type of event you may be doing. If you're looking for more guidance on what to reach for during exercise and how different environments may impact your needs and choices, this blog has a ton of info!
Lastly, don't forget that eating adequate carbs in your everyday diet helps you tolerate more carbs during exercise, too. You can't simply work on your race fueling and neglect your daily needs. This blog will share some carb guidelines for athletes as well as easy ways to get more carbs into your diet.
Practical Tips for Better Gut Tolerance During Exercise
There’s no one-size-fits-all solution for GI issues in endurance sports, but there are a few strategies that I see consistently help athletes improve gut tolerance during training and racing:
Eat consistently and adequately: Chronic low energy intake can negatively impact digestion, recovery, and performance.
Practice your fueling strategy in training: Gut training takes time, especially if you’re increasing carbohydrate intake for longer races.
Be mindful of concentration: Overly concentrated drink mixes or stacking multiple carb sources without adequate fluid can overwhelm the gut.
Adjust for the conditions: Heat, altitude, exercise intensity, and hydration status all influence GI tolerance.
Look beyond the gels: Sometimes a product truly doesn’t work for someone, but a lot of times it’s the bigger picture that matters more
Get professional help for chronic issues: Persistent or severe GI symptoms may require further investigation, and is a great reason to get support from a Sports Dietitian
FAQ: GI Issues in Endurance Athletes
Why do I get diarrhea when I run (aka "runner's trots")? Running diverts blood flow away from the gut and jolts the digestive system in a way that cycling and other sports don't, making loose stools during running very common. Contributing factors include dehydration, too much or too little sodium, hyper-concentrated sports drinks, and taking in more carbohydrates than your gut is trained to handle.
Why do I feel nauseous during a race even when training went fine? Race day may introduce variables that you weren't able to replicate in training, including pre-race nerves, higher intensity, heat, and altitude, all of which can increase GI sensitivity. If nausea hits, try slowing your pace, reducing your intake slightly (but don't stop fueling entirely), and taking smaller bites or sips to help reset the system.
Are my gels or sports drink causing my stomach issues? Possibly, but it's often not that simple. It could also be dehydration, inadequate sodium intake, or not having trained the gut to handle higher carbohydrate intake (notice a theme, here?). That said, hyper-concentrating your drink mix or stacking multiple carb sources (from gels or wherever else) without enough fluid can absolutely cause problems.
How long does gut training take? Ideally, plan for at least two to three months of actively practicing your race fueling strategy before your event. Yes, you can make some progress in a shorter period of time, but there are no shortcuts to fully dialing in your fueling plan.
When should I see a doctor and/or sports dietitian about GI issues during exercise? If you've addressed your fueling plan, hydration, and daily nutrition and are still experiencing significant symptoms, it may be time to dig deeper. Testing like a colonoscopy, endoscopy, or stool testing can help rule out underlying conditions. Working with a sports dietitian is also a great first step, as we can help you figure out where to start and whether further medical evaluation makes sense.
Need Help with GI Issues During Training or Racing?
If you struggle with GI issues when training or racing, or you’re simply looking to build a better fueling strategy so you can feel and perform your best, working with a Sports Dietitian can make a real difference.
In fact, GI issues are one of the most common reasons athletes reach out to me for nutrition support. They can be incredibly frustrating to navigate on your own, but with the right approach and guidance, most athletes can improve their symptoms.
Whether you’re:
Struggling with nausea, cramping, bloating, or diarrhea during exercise
Trying to tolerate higher carb fueling
Unsure how much fluid or sodium you actually need
Training for a marathon, triathlon, or ultra
Or simply feeling overwhelmed by all the sports nutrition information online
…I’d love to support you.
Here’s what one client had to say about working with me:
“Claire was also incredibly persistent in helping me solve a complicated GI situation—I received many emails that started with “oh, and I had one more idea to try…!”—tapping into her deep knowledge of sports and general nutrition and always seeking new information and suggesting new potential solutions. With her help, I have come so far in dialing in both my sports and daily nutrition, kept GI issues under control, and taken my marathon time down 36 minutes in one year, achieving my first Boston- and New York City-qualifying times. I can’t recommend working with Claire enough, and I truly believe it is what has made all the difference in my active lifestyle. Her advice is truly individualized and realistic—something you can’t get from a few slides on Instagram or a generalized guideline."
- Kristina
Here are a few ways to get nutrition support:
Fill out a new client inquiry form for comprehensive 1:1 coaching (limited spots available)
Join my low-cost, low-commitment Fuel for Life Crew membership for just $39/month, (cancel anytime)
Browse my nutrition masterclasses (all are also included in the membership)
Grab my Eat for Endurance Mini Guide Bundle (a collection of 6 mini guides, worksheets, and a bonus supplement resource)
Download my free fueling resources
Meet My Podcast Sponsors
A big thank you to my podcast sponsors, Tailwind Nutrition and Good Ranchers, for supporting this episode!
If you’ve been around here for a while, you’ve definitely heard me talk about Tailwind Nutrition. I’ve personally used their products since 2019, and one of the things I appreciate most, both as an athlete and as a sports dietitian, is how simple they make fueling. Their Endurance Fuel combines carbs, fluids, and electrolytes in one bottle, and it’s one of the few sports nutrition products I truly never get sick of during long runs and rides.
I’m also a big fan of their Recovery Mix for quick post-workout recovery, plus Rapid Hydration for everyday electrolytes without extra carbs. If you’re looking to simplify your fueling strategy and reduce GI drama during exercise, definitely check them out. You can use code EATFORENDURANCE20 for 20% off your first purchase.
I’m also excited to partner with Good Ranchers, a delivery service for high-quality chicken, beef, pork, and seafood. Having convenient, portioned proteins stocked in the freezer makes it so much easier to put together balanced meals that support training and recovery.
Use code IRON for $40 off a one-time box or $100 off your first 3 boxes, plus free protein with your subscription. Make sure you share "The Eat for Endurance Podcast" in your post-purchase survey, so Good Ranchers knows you're supporting the show!
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Disclaimer: All information provided is for educational and entertainment purposes only and is in no way meant to replace individual medical and nutrition recommendations.