Dyspepsia is a disorder characterized by dyspeptic symptoms which are located in the epigastrium and related to digestion of food in the initial part of the digestive system. In functional dyspepsia, unlike organic dyspepsia, there is no underlying organic disease that would cause dyspeptic symptoms. Immune and mucosal function changes, gastric dysmotility, different composition of the gastrointestinal microbiota, and altered central nervous system processing are considered responsible for the onset of the disorder. The diagnosis is based on history, clinical presentation, and exclusion of other organic diseases of the gastrointestinal tract manifested by dyspeptic symptoms. Therapy includes eradication of Helicobacter pylori infection, proton pump inhibitors, prokinetics, neuromodulators, and herbal preparations. Unfortunately, in some patients, this therapy leads to little or no improvement. The prevalence of functional dyspepsia is increasing. It has become one of the more common gastroenterological diagnoses. In order to reduce the costs associated with the diagnosis and treatment of the disorder itself, its mechanisms need to be fully elucidated and thus enable finding appropriate therapy for all patient subgroups.