Dyspepsia is a symptom complex common both in the population and in clinical practice. Persons with dyspeptic symptoms who have not been evaluated are considered to have uninvestigated dyspepsia. If, after investigation, no structural or biochemical explanation is identified to explain the person's symptoms, the diagnosis of functional dyspepsia is made. While substantial efforts have been made to provide symptom-based criteria for the diagnosis of functional dyspepsia, the etiology and natural history of the disorder remains elusive. Population-based studies have often had difficulty distinguishing functional dyspepsia from irritable bowel syndrome. Clinically, there is clearly substantial overlap and many persons with functional dyspepsia either present with symptoms consistent with the irritable bowel syndrome or will develop such symptoms at a later date. Even if one can accept functional dyspepsia as an entity separate from irritable bowel syndrome, it is clearly a heterogeneous disorder. Unfortunately attempts using different strategies to subcategorize functional dyspepsia have not made progress with respect to elucidating pathophysiology or directing therapy. Importantly, most persons with functional dyspepsia experience symptom variability resulting in subgroup reassignment over time. Persons presenting with functional dyspepsia will likely remain symptomatic over time. Sadly, at the present time, gastroenterologists have little ability to predict what those symptoms will be, to understand the mechanism for their existence or to offer therapies that offer a reasonable likelihood of success based on a pathophysiologic rationale.