Functional dyspepsia (FD) is a highly prevalent disorder that affects more than 10% of the population. In the past decade, the theoretical underpinning of the concept of FD has begun to change, in light of new data on the underlying pathophysiological mechanisms of this disorder, with a focus on the duodenum. The Rome IV criteria, published in 2016, note that gastroesophageal reflux disease and irritable bowel syndrome overlap with FD more than expected by chance, suggesting that they may be part of the same disease spectrum. Infection by Helicobacter pylori (H. pylori) may explain a minority of cases of FD and in the Rome IV criteria H. pylori-associated dyspepsia (defined as symptom relief after eradication therapy) is considered a separate entity. Duodenal inflammation characterized by increased eosinophils and in some cases mast cells, may impair the intestinal barrier. Post-infectious gastroenteritis is now an established risk factor for FD. Other risk factors may include atopy, owning herbivore pets and exposure to antibiotics, together with gastroduodenal microbiome disturbances. Small bowel homing T cells and increased cytokines in the circulation occur in FD, correlating with slow gastric emptying, and a possible association with autoimmune rheumatological disease supports background immune system activation. A genetic predisposition is possible. FD has been linked to psychological disorders, but in some cases psychological distress may be driven by gut mechanisms. Therapeutic options are limited and, aside from responders to H. pylori eradication, provide only modest and temporary relief. Advances in understanding FD may alter clinical practice, and the treatment of duodenal inflammation or microbiome alterations may lead to a cure for a subset of these patients in the future.