Numerous surveys of athletes reveal high rates of exertional abdominal pain and gastrointestinal dysfunction. These complaints often are thought to be self-limiting and benign, and they may be mediated by physiological changes that take place in the gastrointestinal tract. However, when these complaints interfere with an athlete's training or competition, it is important to evaluate for underlying pathology. The goal of this article will be to briefly describe the relevant exercise-associated changes of the gastrointestinal tract and provide a differential diagnosis and a proposed mechanism of evaluation of exertional abdominal pain. The etiologies most frequently written about include exercise-associated transient abdominal pain (ETAP or stitch), reflux, diarrhea, ischemia, and musculoskeletal pain. Less common etiologies include cardiorespiratory disease, and rare occurrences of hypoferritinemia, congenital supernumerary ligaments of the gallbladder, cholangitis, and pancreatitis have been published as case reports.