Physical exercise can be both beneficial and harmful for the gastrointestinal tract in a dose-effect relationship between its intensity and health. Mild-to-moderate intensity exercises play a protective role against colon cancer, diverticular disease, cholelithiasis and constipation, whereas acute strenuous exercise may provoke heartburn, nausea, vomiting, abdominal pain, diarrhea and even gastrointestinal bleeding. This review focuses on mechanisms involved in those symptoms and their associations with type of exercises in humans. One quarter to one half of elite athletes are hampered by the gastrointestinal symptoms that may deter them from participation in training and competitive events. Vigorous exercise-induced gastrointestinal symptoms are often attributed to altered motility, mechanical factor or altered neuroimmunoendocrine secretions. Training, lifestyle modifications, meal composition, adequate hydration and avoidance of excessive use of some medications are the recommendations. Strenuous exercise and dehydrated states would be the causes of gastrointestinal symptoms referred by 70% of the athletes. Gut ischemia would be the main cause of nausea, vomiting, abdominal pain and (bloody) diarrhea. The frequency is almost twice as high during running than during other endurance sports as cycling or swimming and 1.5-3.0 times higher in the elite athletes than the recreational exercisers.