Physical exercise is probably both beneficial and harmful for the gastrointestinal tract, depending partly on the training intensity. On the one hand, gastrointestinal symptoms such as heartburn, chest pain, nausea, vomiting, abdominal cramps, side ache and diarrhoea are common during heavy exercise. On the other hand, physical activity seems to protect from colon cancer, cholelithiasis and diverticular disease. Constipation has been shown to be related to inactivity. Despite this, no overwhelming evidence exists for a positive effect of physical exercise as a treatment option for chronic constipation. The reasons behind these somewhat discrepant effects are not understood fully. Altered gastrointestinal blood flow, effects on gastrointestinal motor function, neuroendocrine changes and mechanical effects are probably involved. Conflicting results exist regarding the effects of physical activity on gastrointestinal motility. Modern technologies now make motility studies in various parts of the gastrointestinal tract possible. More studies are needed to understand better the effects of physical exercise on the gastrointestinal tract. In particular, the relationship between the training intensity and duration and positive and negative alterations in gastrointestinal physiology needs to be addressed further.