Stomach ache while running? How to train your gut too

I remember well how it felt during my first marathons, and sometimes even before that during the long training runs. Somewhere between kilometres 10 and 15, my stomach would start to protest. A heavy feeling, as if there was a stone in there, bobbing with every step. Gaseousness that I could barely control. Stomach cramps that worsened with every stride. And the urgent need to find a toilet, at a time when you least want to be dealing with that.

I'm certainly not alone in that. Stomach complaints are one of the most common problems for endurance athletes, with their own nickname: runner's gut. And yet, it's barely spoken about. You grit your teeth, hope it passes, and would rather not talk about it in the changing room.

But there is much more to say about it, and more that can be done, than most athletes know.

Why do your bowels complain during running?

Your body is clever. The moment you start exercising, it decides where blood is most needed: in your muscles. They get priority. Your intestines are temporarily pushed to the background: reduced blood flow, less capacity to process food and fluids. This slows down stomach emptying and causes bloating or nausea, especially during prolonged exertion or heat.

With a gentle 30-minute steady run, you won't notice much. But the longer the exertion lasts, an hour of running or more, a long bike ride, a triathlon, the more your intestinal function comes under pressure.

What's more, running is mechanically quite aggressive on your intestines. Every step is a small jolt, and over a long run, that really adds up. This constant vibration irritates the bowel contents and can speed up transit, leading to a different type of complaint than reduced blood flow. While the latter leads to nausea and bloating, the jarring of running actually causes flatulence, sudden urgency, and diarrhoea. That's also why runners suffer from this far more than cyclists, who sit comfortably on a saddle while their legs move.

And then there's the stress. The morning before a match, many athletes recognise it as a combination of nerves and frequent toilet visits. That's no coincidence. Nerves directly affect your gastrointestinal system, and on match day, that system is on high alert.

How often does it actually occur?

Much more often than you might think. Research shows that 30 to 50% of all endurance athletes regularly suffer from digestive problems (https://pubmed.ncbi.nlm.nih.gov/28332114/), and for long-distance runners, this rises to 90%. The link with distance and duration is clear: the longer the exertion, the greater the likelihood. If this sounds familiar, it’s not down to a weak stomach. It’s a physiological response to exertion, and there are steps you can take to manage it.

What makes it worse?

The same causes can be identified in most athletes. Eating too much just before exercise is one of them. A large meal three-quarters of an hour before your training is asking for trouble, because your body is still busy digesting when you're already running. Fibre and fat work the same way: excellent nutrition, but hard on your gut at the wrong moment. A slice of wholemeal bread with peanut butter an hour before a long training session can cause significant stomach upset.

Energy gels are a chapter in themselves. They contain concentrated sugars that draw fluid into your gut if you don't drink enough water with them, which can cause cramps and diarrhoea. The intensity also plays a role: the harder you run, the less blood flows to your gut. Food that you normally tolerate well can then still cause problems. Not because there's anything wrong with the gel, but because your body is under more pressure at that moment. Dehydration makes it all even more erratic.

Perhaps the most classic mistake is trying new gels or sports drinks on race day. You've bought something new, it's ready to go, and you think: today's the day I'll try it. What your gut doesn't know, it doesn't trust.

What can you do about it?

Truth be told, the basics aren't that complicated. Eat your main meal two to three hours before your training session or competition. If you want a small snack in between, choose something easily digestible: a slice of ripe banana, a rice cake, or some white bread with honey.

Test every gel and every sports drink you intend to use in a race multiple times during training. Don't do it just once as an experiment, but repeatedly. Always take a sip of water with it, never a gel without fluid. Also, drink enough throughout the day, not just during exercise itself.

And try to stick to a regular routine for eating and training. It sounds boring, but your gut loves predictability. The same applies to pre-match nerves: a calm warm-up or a few minutes of mindful breathing helps more than you think, as nerves literally work their way into your stomach.

Your gut is trainable! And that's the big insight

This is the point that surprises most athletes, and the one I most want to impart.

Sports nutrition scientist Asker Jeukendrup, one of the most cited researchers in the field of endurance sports and nutrition, states in his paper Training the Gut for Athletes (https://pubmed.ncbi.nlm.nih.gov/28332114/it's seen that your gut can adapt, just as your muscles do. Targeted gut training improves the absorption of carbohydrates and fluids during exercise, and can reduce or even eliminate discomfort. The idea is as simple as it is little applied by athletes: you don't just train your legs, you also train your gut.

Your intestines contain transport proteins that absorb carbohydrates from food. With regular exposure to carbohydrates during exercise, these transport proteins become more active. Your intestines literally become more efficient at processing fuel. The same applies to fluid: those who consistently train with slightly more sports drink than is strictly necessary find that their stomach tolerates it better over time.

For practice, this mainly means: consistently practise your race nutrition during training. The same gels, the same timing, the same amounts. Start small, half a gel and a modest amount of sports drink on your long training sessions, and build that up gradually each week. What initially feels uncomfortable will gradually become normal.

The beauty is that this doesn't have to take months. Research by Costa et al. (https://pubmed.ncbi.nlm.nih.gov/28508559/Even after just two weeks of targeted bowel training, they saw a significant reduction in symptoms. Your bowels adapt faster than you think, you just need to give them the chance.

When should you look further?

The adjustments in this blog help most athletes a great deal. However, if complaints persist despite improved nutrition and timing, also occur outside of sport, or are accompanied by blood loss or unexplained weight loss, a GP or dietitian is the right step. This blog is not medical advice and does not replace professional guidance.

Conclusion

Bowel issues during running or cycling are annoying, but they're not unavoidable. In many cases, they can be traced back to timing, dietary choices, or insufficient adaptation. And Jeukendrup's great insight is simple but powerful: your gut is trainable. With a few weeks of targeted practice, you can get it on board, so you can simply run during your next race without your mind already being focused on the nearest toilet halfway through.

Would you like to learn how nutrition can work better for your sport? Then sign up for the free Masterclass Sport Nutrition Basics. Practical, accessible, and hassle-free. Sign up via https://twindo-sportvoedingsadvies.nl/gratis-masterclass-sportvoeding-basics/#aanmelden