Gastrointestinal (GI) complaints are common among athletes with rates in the range of 30% to 70%. Both the intensity of sport and the type of sporting activity have been shown to be contributing factors in the development of GI symptoms. Three important factors have been postulated as contributing to the pathophysiology of GI complaints in athletes: mechanical forces, altered GI blood flow, and neuroendocrine changes. As a result of those factors, gastroesophageal reflux disease (GERD), nausea, vomiting, gastritis, peptic ulcers, GI bleeding, or exercise-related transient abdominal pain (ETAP) may develop. GERD may be treated with changes in eating habits, lifestyle modifications, and training modifications. Nausea and vomiting may respond to simple training modifications, including no solid food 3 hours prior to an athletic event. Mechanical trauma, decreased splanchnic blood flow during exercise, and non-steroidal anti-inflammatory drugs (NSAID) contribute to gastritis, GI bleeding, and ulcer formation in athletes. Acid suppression with proton-pump inhibitors may be useful in athletes with persistence of any of the above symptoms. ETAP is a common, poorly-understood, self-limited acute abdominal pain which is difficult to treat. ETAP incidence increases in athletes beginning a new exercise program or increasing the intensity of their current exercise program. ETAP may respond to changes in breathing patterns or may resolve simply with continued training. Evaluation of the athlete with upper GI symptoms requires a thorough history, a detailed training log, a focused physical examination aimed at ruling out potentially serious causes of symptoms, and follow-up laboratory testing based on concerning physical examination findings.