This article presents an overview of some of the more commonly encountered disorders of the gastrointestinal tract that are seen in athletes. As with other medical conditions, the clinician can often be blinded by an athlete's physical activity and overlook underlying disease. Fortunately, most of the maladies described here are amenable to medical treatment, and with proper diagnosis and management the athlete should be able to achieve his or her maximal athletic performance. The study of the gastrointestinal tract and exercise is still in its early stages and was prompted by the need to explain clinical observations. Although some questions have been answered, the positive and negative effects of physical activity on the gastrointestinal tract have many avenues of research left to explore.