Despite reports of gastrointestinal (GI) symptomology in athletes since at least the 1980s, GI health has not received sufficient interest in sports nutrition until recently. The incidence of GI symptoms is most frequent in endurance sport participants, especially runners, but it has also been reported in other sports, including team events. Possible causes may include hypoperfusion of the GI tract during exercise, due to splanchnic redistribution of blood flow, causing gut ischaemia, which can result in disruption to the intestinal barrier. It is also important to understand why athletes experience GI symptoms at rest, which may relate to nutrition and lifestyle patterns, stress, the use of certain medications, and others. The human microbiome is a vital part of GI health, which ‘cross-talks’ with the brain and mitochondria, and many other aspects of an athlete’s physiology. Microbial diversity has been shown to be improved with exercise participation, but stresses of training and competition can, conversely, deplete microbial health. Many nutrition and lifestyle strategies for improved GI health are already in use within integrative health practices, and can be applied into a sport and exercise context, as demonstrated in a case study of a recreational trail runner.