Upper gastrointestinal symptoms account for a considerable proportion of all primary care visits, and about 80% of those patients with epigastric pain have a normal endoscopy. Functional dyspepsia is a common gastrointestinal problem with complex pathophysiology and pathogenesis. The pathophysiological abnormalities underlying functional dyspepsia include impaired gastric emptying and accommodation as well as gastroduodenal hypersensitivity. Multiple pathogenetic factors in functional dyspepsia are related to the presence of Helicobacter pylori, post-infectious inflammation, psychosocial factors, and genetic predisposition. Moreover, environment, dietary factors, and lifestyle might be pathogenic to functional dyspepsia. These factors with multiple interactions contribute complex manifestation of functional dyspepsia. This presentation aims to provide an updated and integrated overview of the pathophysiological mechanisms in functional dyspepsia. Better understanding of the pathophysiology leading to functional dyspepsia will help improve clinical management of this common gastrointestinal disorder.