Functional dyspepsia and irritable bowel syndrome are currently considered to be two separate nosological entities. However, the overlap of symptoms and the evidence of a number of common pathophysiological characteristics suggest that functional dyspepsia and irritable bowel syndrome may be different presentations of the same disorder. In this review, we critically appraise points in common, as well as differences, in the epidemiology, pathophysiology and response to treatment of functional dyspepsia and irritable bowel syndrome. Population-based studies and large case series show that one- to two-thirds of subjects with irritable bowel syndrome have symptoms that overlap with functional dyspepsia. Symptom analyses have generally failed to support functional dyspepsia and irritable bowel syndrome as separate entities. An exaggerated motor response to meals, delayed gastric emptying and abnormal small bowel and colonic transit can all be found in subsets of functional dyspepsia and irritable bowel syndrome, and are not exclusive to either condition. Visceral hypersensitivity is a common feature to both entities and seems unlikely to be site or disease specific. There is good evidence for the post-infectious development of irritable bowel syndrome, and this may also apply in functional dyspepsia. Psychiatric comorbidities are similar in functional dyspepsia and irritable bowel syndrome. Several common drug classes (prokinetics, visceral analgesics, psychoactive agents) may similarly improve both functional dyspepsia and irritable bowel syndrome symptoms. The evidence available suggests that at least subsets of functional dyspepsia and irritable bowel syndrome represent different manifestations of a single entity. The identification of common pathophysiological targets for therapy should be pursued in future research.