Gastrointestinal Issues During Endurance Exercise: Causes and How to Train Your Gut

Stomach and bowel problems can disrupt even the most carefully planned endurance event.

An athlete may know how much carbohydrate they need but still struggle with bloating, nausea, reflux, cramps or an urgent need to use the toilet during training and competition. In more severe cases, gastrointestinal symptoms can make it difficult to continue exercising or consume enough fuel and fluid.

These issues are common. Research generally suggests that approximately 30–50% of athletes experience gastrointestinal complaints during exercise, although rates vary depending on the sport, distance, intensity, conditions and how symptoms are measured.

The good news is that some gastrointestinal issues can be reduced through appropriate nutrition choices, a well-practised hydration strategy and progressive gut training.

However, symptoms are rarely caused by one factor alone. Understanding why they occur is the first step towards developing a fuelling plan that works in the real world.

What gastrointestinal symptoms can athletes experience?

Exercise-associated gastrointestinal symptoms can affect the upper or lower digestive tract.

Upper gastrointestinal symptoms may include:

• Reflux or heartburn

• Nausea

• Vomiting

• Belching

• Stomach fullness

• Bloating

• Upper abdominal discomfort

Lower gastrointestinal symptoms may include:

• Cramping

• Flatulence

• An urgent need to use the toilet

• Loose stools or diarrhoea

• Lower abdominal pain

• Intestinal bleeding in more serious cases

Symptoms may occur during exercise, immediately afterwards or later in the recovery period.

Although many exercise-related symptoms are mild, severe or persistent symptoms should not automatically be dismissed as a normal part of endurance sport.

Why do gastrointestinal issues occur during endurance exercise?

Exercise-related gut problems are usually influenced by a combination of physiological, mechanical and nutritional factors.

• Blood flow is redirected away from the gut

• Running creates additional mechanical stress

• Heat can increase gastrointestinal strain

• Dehydration may worsen symptoms

• Carbohydrate intake may exceed current tolerance

• The type and concentration of carbohydrate matter

• Pre-exercise food choices may contribute

  

What is gut training?

Gut training involves repeatedly practising the nutrition and hydration strategy you plan to use during competition.

Just as muscles adapt to repeated training, parts of the gastrointestinal system can also adapt to regular exposure to carbohydrate, food and fluid during exercise.

Potential adaptations may include:

• Improved comfort with food or fluid in the stomach

• Reduced feelings of fullness

• Improved carbohydrate absorption

• Reduced carbohydrate malabsorption

• Fewer gastrointestinal symptoms

• Greater confidence in the race plan

• An improved ability to consume fuel while exercising

A review of gut training suggests that gastric comfort, nutrient absorption and tolerance can be influenced by repeated dietary exposure, although the degree of adaptation varies between athletes.

In one study, endurance runners completed two weeks of repeated carbohydrate feeding during running. The carbohydrate group experienced reductions in overall gut discomfort, nausea, upper- and lower-gastrointestinal symptoms and carbohydrate malabsorption.

Gut training can therefore be useful, but it is not a guarantee that every athlete will tolerate extremely high carbohydrate intakes. A systematic review found potential benefits for reducing gut discomfort and carbohydrate malabsorption, but results were not consistent across all studies.

How to train your gut

1. Start below your intended race target

Find out more about how much carbohydrates you should be aiming more here.

Do not immediately jump to the highest carbohydrate guideline for your event.

Begin with an amount you can currently tolerate and gradually increase it during selected training sessions.

For example, an athlete aiming to eventually consume 75-90g of carbohydrate per hour might progress through:

• 30-45g per hour

• 45-60g per hour

• 60-75g per hour

• The intended race target

This is only an example. The appropriate starting point and rate of progression will depend on the athlete, event and current intake.

There is no need to practise very high carbohydrate intakes during every session. Gut training is most useful when incorporated strategically into longer and more race-specific sessions.

2. Practise during relevant training sessions

A race strategy needs to work at race intensity, not only during easy exercise.

Test your plan during:

• Long runs or rides

• Race-pace sessions

• Brick sessions

• Competition simulations

• Training in similar weather conditions

• Sessions completed at a similar time of day

• Training on terrain similar to the race course

A strategy tolerated during a relaxed ride in cool weather may feel very different during a hard run in Singapore’s heat and humidity.

3. Use the same products you plan to race with

Practise with the actual products you intend to use, including:

• Gels

• Sports drinks

• Chews or gummies

• Bars

• Solid foods

• Electrolyte products

• Caffeine

• Water

Different brands can contain different carbohydrate blends, concentrations, textures and sweeteners.

You should also practise how you will carry, open and consume each product while moving.

Race nutrition is partly a physiological challenge and partly a logistical one.

4. Spread your intake across the hour

Many athletes tolerate smaller, more frequent amounts better than a large amount consumed all at once.

For example, an athlete targeting 60 g of carbohydrate per hour might consume approximately:

• 20g every 20 minutes, or

• 30g every 30 minutes

The ideal pattern will depend on the product, sport, course and aid-station availability.

Starting early may also be easier than waiting until energy levels begin to decline and then trying to catch up with several products at once.

5. Practise carbohydrate and hydration together

Carbohydrate and fluid strategies should not be developed separately. A gel may feel comfortable when consumed with water but cause discomfort when taken alongside a concentrated sports drink. Similarly, a drink that works at one concentration may become difficult to tolerate if several gels are consumed at the same time.

When testing your plan, consider:

• Carbohydrate per hour

• Fluid per hour

• Drink concentration

• Timing of gels or foods

• Environmental conditions

• Sweat rate

• Access to water

• Whether products contain caffeine or electrolytes

Practise the entire strategy rather than changing several variables on race day.

6. Test your pre-exercise meal

Gut training does not only involve what you consume during exercise.

The meal and snacks eaten beforehand can influence how comfortable you feel once the session begins.

Consider testing:

• How many hours before exercise you eat

• The size of the meal

• The amount of fibre

• The amount of fat and protein

• The type of carbohydrate

• Whether solid or liquid foods feel better

• How much fluid you consume before starting

Some athletes may benefit from a lower-fibre or lower-fat meal before long, intense or high-impact sessions. However, this should be individualised rather than applied as a permanent restriction.

7. Change one variable at a time

When symptoms occur, athletes often replace several foods and products at once.

This can make it difficult to identify what actually caused the problem.

Instead, change one key variable where possible. For example:

• Reduce the carbohydrate dose taken at one time

• Change the timing of intake

• Adjust the drink concentration

• Increase the amount of water consumed with gels

• Modify the pre-training meal

• Remove an unfamiliar product

• Test a different carbohydrate source

A systematic approach makes it easier to identify patterns.

8. Record your symptoms

After important training sessions, record:

• Exercise duration and intensity

• Carbohydrate consumed per hour

• Fluid consumed per hour

• Products and flavours used

• Timing of each intake

• Pre-exercise food and fluid

• Weather conditions

• Upper gastrointestinal symptoms

• Lower gastrointestinal symptoms

• Energy levels

• Perceived performance

You could rate symptoms from 0–10 and note when they occurred.

For example:

Time	Intake	Symptoms	Severity
0:20	Gel and water	None	0/10
0:40	Sports drink	Mild bloating	2/10
1:00	Gel without water	Nausea	5/10
1:20	Water	Symptoms improved	2/10

This provides more useful information than simply concluding that “gels do not work for me.”

Do you need a low-FODMAP diet?

Some athletes hear about low-FODMAP diets as a solution for exercise-related gut problems.

Reducing selected fermentable carbohydrates may help some athletes with specific symptoms, particularly when there is an underlying gastrointestinal condition. However, a low-FODMAP diet is not automatically appropriate for every endurance athlete.

Unnecessary restriction may:

• Reduce dietary variety

• Make fuelling more difficult

• Compromise carbohydrate intake

• Create anxiety around food

• Mask an underlying medical issue

A short-term, targeted approach may sometimes be appropriate under the guidance of a qualified nutritionist or dietitian. It should not be the first response to every case of bloating, nausea or diarrhoea.

Start by reviewing the basics: meal timing, carbohydrate concentration, hydration, product familiarity, heat exposure and the rate at which intake was increased.

When should you seek medical advice?

Not every gastrointestinal symptom is caused by exercise or nutrition.

Seek medical assessment when symptoms:

• Are severe or becoming progressively worse

• Frequently occur outside exercise

• Persist despite adjusting your nutrition strategy

• Prevent you from eating or drinking adequately

• Are associated with unexplained weight loss

• Include repeated vomiting

• Include blood in the stool

• Include black or tarry stools

• Are associated with severe abdominal pain

• Are accompanied by dizziness, weakness or signs of dehydration

Blood in the stool, unexplained weight loss, persistent vomiting and severe or recurrent abdominal pain should be assessed by a healthcare professional rather than managed solely through dietary experimentation.

Never test a new strategy on race day

Race day is not the time to discover that:

• A gel triggers reflux

• Your sports drink is too concentrated

• Your caffeine dose causes nausea

• Your planned intake is difficult while running

• You cannot access enough water

• Your strategy does not work in hot conditions

• Your pre-race meal is too large or too high in fibre

Train your gut like you train your legs.

The best fuelling plan is not necessarily the one with the highest carbohydrate target.

It is the plan that provides enough fuel for the demands of the event while remaining practical, familiar and tolerable for you.

The take-home message

Gastrointestinal symptoms are common during endurance exercise and are usually influenced by several overlapping factors.

These may include:

• Reduced blood flow to the gut

• Mechanical impact

• Heat and hydration status

• Pre-exercise food choices

• Carbohydrate concentration

• Large or unfamiliar fuel intakes

• Individual gastrointestinal sensitivity

Athletes may be able to improve tolerance by progressing their carbohydrate intake gradually, practising under race-specific conditions and testing their nutrition and hydration plans together.

Track what happens, adjust systematically and seek medical advice when symptoms are severe, persistent or occur outside exercise.

Not sure what carbohydrate intake you should be working towards? Read: How Much Carbohydrate Do Endurance Athletes Need During Exercise?

References

Costa, R. J., Gaskell, S. K., Henningsen, K., Jeacocke, N. A., Martinez, I. G., Mika, A., ... & Young, P. (2025). 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: RJS Costa et al. Sports Medicine, 55(5), 1097-1134.

Costa, R. J., Snipe, R. M., Kitic, C. M., & Gibson, P. R. (2017). Systematic review: exercise‐induced gastrointestinal syndrome—implications for health and intestinal disease. Alimentary pharmacology & therapeutics, 46(3), 246-265.

de Oliveira, E. P., Burini, R. C., & Jeukendrup, A. (2014). Gastrointestinal complaints during exercise: prevalence, etiology, and nutritional recommendations. Sports medicine, 44(Suppl 1), 79-85.

Jeukendrup, A. E. (2017). Training the gut for athletes. Sports Medicine, 47(Suppl 1), 101-110.

Miall, A., Khoo, A., Rauch, C., Snipe, R. M. J., Camões‐Costa, V. L., Gibson, P. R., & Costa, R. J. (2018). Two weeks of repetitive gut‐challenge reduce exercise‐associated gastrointestinal symptoms and malabsorption. Scandinavian Journal of Medicine & Science in Sports, 28(2), 630-640.

Mlinaric, J., & Mohorko, N. (2025). Nutritional strategies for minimizing gastrointestinal symptoms during endurance exercise: systematic review of the literature. Journal of the International Society of Sports Nutrition, 22(1), 2529910.

Morton, J. P., Fell, J. M., Gonzalez, J. T., Hearris, M. A., Podlogar, T., Pugh, J. N., & Wallis, G. A. (2026). From Metabolism to Medals: Contemporary Perspectives and Revisiting Carbohydrate Guidelines for Fuelling Endurance Athletes During Exercise. The Journal of nutrition, 101442.