Gels get blamed for a lot of stomach problems in endurance sport. Sometimes that blame is fair, but often the issue is not the gel itself, it's the combination of how much carbohydrate you are consuming, how quickly you are taking it, what else you are drinking, the intensity of the session, and whether your gut has actually been trained for that strategy.

Running already places stress on the gastrointestinal system: blood flow is redirected towards working muscles and the skin, and the repeated movement that running requires can add further disruption. Heat, dehydration and race intensity on top of this can also impact digestion.[1,2]

Overloading carbs.

Gels are concentrated sources of carbohydrate, which is exactly why they are used for performance. Problems can start when the amount you're consuming is higher than your gut can comfortably absorb. If carbohydrate remains in the intestine instead of being absorbed, it can contribute to bloating, nausea, cramping and diarrhoea.[3]

This is why jumping from one gel an hour in training to three gels an hour on race day can go badly. Your fuelling target needs to match both the demands of the event and what you have trained your gut to tolerate.

It is also important to count everything. If you are aiming for 90g of carbohydrate per hour and take three 30g gels, you are already at 90g. If your sports drink adds another 30g per hour, your actual intake is 120g.

Carb source.

At higher carbohydrate intakes, the type of carbohydrate you are using is important. Glucose primarily uses the intestinal transporter SGLT1, while fructose uses GLUT5. Combining the two allows your body to use more than one absorption pathway, which can improve overall absorption especially with higher intakes.[4]

For this reason, many endurance products combine glucose or maltodextrin with fructose rather than relying on one carbohydrate source alone. We go into this in more detail in our article on glucose-to-fructose ratios and the shift from 2:1 towards 1:0.8.

This does not necessarily mean fructose will agree with every athlete in every amount - individual tolerance should still be tested, particularly when carb intake is already high.

Fluid intake.

Some gels are designed to be taken with water, and swallowing a highly concentrated gel without enough fluid around it can make things harder on the gut. Highly concentrated carbohydrate solutions can slow gastric emptying and increase gastrointestinal discomfort.[3] The amount of fluid required depends on the product, so it's important to check how each gel is designed to be used.

For Aussie athletes, or any athlete competing in high temperatures, hot conditions and dehydration can increase gastrointestinal stress during prolonged exercise. A fuelling strategy that feels fine on a cool training morning may feel very different during a hot race [2,5], so these factors should be taken into account before race day.

Spread your gels out.

If your target is 90g per hour, that does not mean taking 90g at once at the top of every hour.

For example, an athlete using 30g gels might take one roughly every 20 minutes. Someone targeting 60g per hour might take one every 30 minutes. The exact interval is less important than having a regular pattern that is practical and well tolerated. Waiting until you feel flat and then trying to catch up with a large amount of carbohydrate is much harder on the gut than following a practiced plan from the start.

Your gut may need training.

Research in the endurance space has shown that repeated carbohydrate feeding during training can reduce gastrointestinal symptoms and improve carbohydrate absorption.[6,7] In one study, runners completed two weeks of gut training while consuming 90g of carbohydrate per hour and experienced less GI discomfort, nausea and leftover unabsorbed carbohydrates afterwards.[6]

So if 90g per hour currently leaves you feeling sick, bloated or cramping, try building towards that amount gradually rather than blaming the gel itself.

Practise the strategy you plan to race with.

Your long runs should be where you test the actual plan: the same gels, the same hourly carbohydrate target, similar fluid intake, and ideally some sessions at your intended race intensity.

If problems continue, change just one variable at a time. The issue could be total carbohydrate intake, the type of carbohydrate, fluid intake, caffeine, heat, or how quickly you are consuming everything. Gels themselves are not inherently worse for gut comfort than other carbohydrate formats when used appropriately.[8] The problems typically come from the overall strategy.

Work out how much carbohydrate you actually need, account for what is coming from drinks as well as gels, and practise that intake until it feels familiar.

References.

1. Rehrer NJ, Meijer GA. Biomechanical vibration of the abdominal region during running and bicycling. Journal of Sports Medicine and Physical Fitness.
2. Costa RJS, Snipe RMJ, Kitic CM, Gibson PR. Systematic review: exercise-induced gastrointestinal syndrome—implications for health and intestinal disease. Alimentary Pharmacology & Therapeutics. 2017;46(3):246–265.
3. de Oliveira EP, Burini RC. Carbohydrate-dependent, exercise-induced gastrointestinal distress. Nutrients. 2014;6(10):4191–4199.
4. Jeukendrup AE. Carbohydrate and exercise performance: the role of multiple transportable carbohydrates. Current Opinion in Clinical Nutrition and Metabolic Care. 2010;13(4):452–457.
5. Sports Dietitians Australia and Ultra Sports Science Foundation. Joint Position Statement: A Practitioner Guide to the Prevention and Management of Exercise-Associated Gastrointestinal Perturbations and Symptoms. 2025.
6. Miall A, Khoo A, Rauch C, et al. Two weeks of repetitive gut-challenge reduce exercise-associated gastrointestinal symptoms and malabsorption. Scandinavian Journal of Medicine & Science in Sports. 2018;28(2):630–640.
7. Costa RJS, Miall A, Khoo A, et al. Gut-training: the impact of two weeks repetitive gut-challenge during exercise on gastrointestinal status, glucose availability, fuel kinetics, and running performance. Applied Physiology, Nutrition, and Metabolism. 2017;42(5):547–557.
8. Guillochon M, Rowlands DS. Solid, Gel, and Liquid Carbohydrate Format Effects on Gut Comfort and Performance. International Journal of Sport Nutrition and Exercise Metabolism. 2017;27(3):247–254.