Stomach trouble during long, hard exercise is not a personal failing and it is not rare. A 2025 joint position statement from Sports Dietitians Australia and the Ultra Sports Science Foundation puts the reported range at “4% after marathon competition” to “≥ 93% in response to ultra-endurance event participation.” The mechanisms are reasonably well described. The fixes are thinner than the supplement aisle suggests, and this article is explicit about which is which.
The short version
- The cause is mostly blood flow. Hard exercise redirects circulation away from the gut, and the drop begins around 70–80% of VO₂max.
- It reverses fast. In a controlled study, gut perfusion returned close to baseline within an hour of stopping.
- 60 g of carbohydrate per hour is a transporter limit, not a rule of thumb. Beyond it, mixing glucose with fructose is what lets you go higher.
- Do not exceed 90 g/h. Current guidance stops there; 120 g/h raises oxidation but has not been shown to improve performance.
- Losing more than 2% of body mass consistently reduces performance — and dehydration itself slows gastric emptying and increases nausea.
- Probiotics are not the answer here. Of 24 studies measuring performance, 17 found nothing.
How common it actually is
The honest answer is a range, not a number. A 2025 scoping review found “11.5–80.0% of athletes reporting at least one gastrointestinal symptom”, with 24.5–52.0% reporting symptoms during exercise or competition specifically.
| Symptom | Reported prevalence |
|---|---|
| Flatulence | 2.8–48% |
| Stomach cramps or rumbling | 5.1–37% |
| Bloating | 2.5–32% |
| Diarrhoea and urge to defecate | Both more common during exercise than at rest |
Why so wide? The reviewers say it directly: the variation “may be due to heterogeneity in screening tools”, and they call for standardised methods for assessing gastrointestinal issues in athletes. Treat any article quoting one confident percentage with suspicion.
What is actually happening
The current framework calls this exercise-induced gastrointestinal syndrome, and describes two main routes. The circulatory route is blood: exercise redistributes circulation to working muscle, producing splanchnic hypoperfusion and gut ischaemia. The neuroendocrine route is the stress response, via sympathetic activation and stress hormones. Metabolic acidosis at high intensity and hypoglycaemia contribute to nausea, and mechanical jostling adds to it in running.
There is a reasonably specific intensity marker. A 2021 review in Frontiers in Nutrition states that “the decrease in splanchnic blood flow occurs at around 70–80% of the maximum oxygen consumption (VO2max) during exercise”, and that intensities at or above roughly 70% of maximum capacity sustained beyond an hour can increase intestinal permeability. Hyperthermia above 40 °C and local ischaemia both disturb the tight junctions between gut cells.
A controlled human study measured it directly. After 60 minutes of cycling at 70% of maximum workload, gut perfusion fell measurably, plasma I-FABP — a marker of damage to intestinal cells — roughly doubled, and the degree of hypoperfusion correlated with the amount of small-intestinal damage. The reassuring half of the same result: perfusion “approximated baseline within 1 hour after exercise.”
What the researchers will not claim, and neither will we. The same 2021 review states that “it is still uncertain what the acute and chronic effects of exercise are on intestinal injury” and that an exercise threshold for gut permeability “is still uncertain.” So: a mechanism, yes. A precise number at which your gut breaks, no.
Carbohydrate during exercise: where the 60 g limit comes from
The familiar advice of about 60 g of carbohydrate per hour is not a tradition — it is the ceiling of a transporter. At that intake, “the sodium-glucose linked transporters (SGLT1) in the small intestine become saturated.” Everything above it has to enter by a different door, which is why fructose is added: it uses a separate transporter.
| Session length | Carbohydrate guidance | Form |
|---|---|---|
| Up to about 3 hours | Up to 60 g per hour | Glucose, glucose polymers, or glucose–fructose |
| Longer than about 2.5 hours | 60–90 g per hour | Glucose–fructose mix, since SGLT1 is saturated |
| Any | Not more than 90 g per hour | Current guidance does not advise going higher |
Two details matter for comfort. The traditional 2:1 glucose-to-fructose ratio has been challenged: a ratio closer to 1:0.8 appears superior “both from the perspective of oxidation efficiency … as well as gut comfort.” And mixed-carbohydrate drinks produce fewer gastrointestinal issues than single-source ones. As for pushing to 120 g/h — oxidation rises, but endogenous carbohydrate is not further spared, and performance evidence remains inconclusive.
“Gut training” — real, and thinly evidenced
Gut training means repeatedly exposing the gut to nutrients before and during exercise so it tolerates more of them. It is a genuine practice with a genuine rationale. It is also a small literature: a 2023 systematic review in Sports Medicine screened 304 studies and included eight.
What those eight did: carbohydrate during exercise at 30–90 g/h, over 4 to 28 days. What they found, stated exactly as the reviewers did:
- Carbohydrate malabsorption fell by 45–54% in two studies — and did not change significantly in a third.
- Gut discomfort decreased by an average of 47% and 26% in two protocols.
- Across the set, significant improvement in gastrointestinal symptoms was seen in two studies, with unclear results in four.
Even the researcher most associated with the idea is careful: writing in Sports Medicine, Jeukendrup notes that “very few studies have directly investigated such effects of ‘nutritional training of the stomach’.” Practise your race fuelling in training — it is sensible and costs nothing. Do not expect a documented percentage of improvement.
Hydration, and why it is a gut issue too
The National Athletic Trainers’ Association position statement is direct: “Performance was consistently reduced when hypohydration met or exceeded 2% body mass loss.” The recommendation is to finish exercise below that.
| Measure | Figure |
|---|---|
| Adult sweat rate during exercise | 0.5 to 4.0 L per hour |
| Sodium lost in sweat | 0.2 to 7.3 g per hour |
| Practical drinking pattern | About 200 mL every 15 to 20 minutes |
| Carbohydrate concentration for fluid absorption | Between 3% and 8% |
The gut connection is direct. Gastric emptying is altered by fluid volume, osmolality, carbohydrate concentration, exercise intensity and the extent of dehydration, and “exercise at greater than 80% of VO2max may decrease the rate of gastric emptying.” An experimental study found that at 3% body-mass loss, gastric emptying slowed and nausea and epigastric cramps rose significantly — and the change in emptying correlated closely with the change in nausea. Notably, the same study found dehydration did not change intestinal permeability or glucose absorption. Dehydration makes your stomach feel worse before it damages anything.
Probiotics for athletes: what the numbers say
This is where marketing and evidence part company. The International Society of Sports Nutrition’s own position stand reports that of 24 studies assessing a metric of athletic performance, 17 reported a null effect and 7 reported significant improvement — and the stand itself says the potential benefits “require validation in more rigorous human studies and in an athletic population.”
A 2023 systematic review reaches the same place: most studies reported positive effects, but “the heterogeneity of the available studies does not allow us to draw definite conclusions on this issue.” And the 2025 joint position statement goes further, listing probiotic supplementation among the interventions that have reported negative outcomes for exercise-associated gut symptoms.
The parts of the ISSN stand that are positively worded concern upper respiratory tract infections, gut barrier integrity and recovery from muscle-damaging exercise — not performance. If you use a probiotic, use it for a specific documented reason, match the exact strain, and do not expect it to fix race-day stomach trouble.
FAQ
Why does my stomach only hurt on long runs, never in the gym?
Because the mechanism is duration and intensity dependent. Splanchnic blood flow starts to drop around 70–80% of VO₂max, and permeability changes have been observed at roughly 70% of maximum capacity sustained beyond an hour. A 40-minute gym session rarely reaches that combination.
How much carbohydrate can I take during a race?
Up to 60 g per hour from glucose alone; 60–90 g per hour for sessions beyond about 2.5 hours, using a glucose–fructose mix. Current guidance does not advise exceeding 90 g per hour.
Does gut training work?
The direction of the evidence is favourable and the evidence base is small — eight studies in total, with malabsorption improving in two, unchanged in one, and symptom outcomes unclear in four. Practising your fuelling is worth doing; a guaranteed result is not on offer.
Will a probiotic stop race-day diarrhoea?
There is no good evidence for that. Seventeen of 24 performance studies found nothing, and the 2025 position statement lists probiotics among interventions with reported negative outcomes for gut symptoms.
What actually helps most?
The 2025 position statement names carbohydrate and protein intake and staying euhydrated before and during exercise among the strategies with mostly consistent beneficial outcomes. Start hydrated, keep the loss under 2%, use a mixed-carbohydrate drink at 3–8% concentration, and rehearse it in training.
Where this fits
The general picture — fibre, fermented food, prebiotics and probiotics, and what packages may legally claim — is in our guide to gut health and nutrition. The mechanics of digestion itself are in how your gut absorbs nutrients. For the sodium side of sweat losses, see our sodium intake guide.
Every figure here is linked to its source in the text: a 2025 joint position statement in Sports Medicine, the National Athletic Trainers’ Association position statement, the International Society of Sports Nutrition position stand, and peer-reviewed systematic reviews and controlled studies in Sports Medicine, Frontiers in Nutrition, PLOS ONE and the European Journal of Applied Physiology. Checked against those sources on 1 September 2026. Educational information, not medical advice — see our medical disclaimer.
This content is for educational purposes only and is not medical advice. Always consult a qualified healthcare professional for personalised guidance.
