Patients with dyspepsia/functional dyspepsia (FD) show frequent overlapping of other gastrointestinal (GI) diseases, such as irritable bowel syndrome, and non-GI diseases, in addition to internal subgroup overlapping. These overlap patients have more frequent or more severe symptoms, poorer health-related quality of life and higher somatization scores, and they are more likely to experience anxiety, depression or insomnia compared to non-overlap patients. The higher prevalence of overlap in patients with dyspepsia/FD is not by chance, indicating common pathogeneses, including visceral hypersensitivity, altered GI motility, infection, and stressful early life events. There are few clinical trials targeting overlap in patients with dyspepsia/FD, and no therapeutic strategy has been established. Further studies in this research area are needed. In this review, we describe the epidemiology, pathogenesis and treatment of overlap in patients with dyspepsia/FD.