Functional, or non-ulcer, dyspepsia (FD) and non-erosive reflux disease (NERD), or endoscopy negative reflux disease are common reasons for referral to both the primary care physician and the gastroenterologist. Their aetiology remains largely obscure but both clinical and basic research have revealed much to suggest that these two disease entities are inextricably linked and may represent part of the same disease process. Several theories have been proposed to explain the pathophysiology of functional dyspepsia, including visceral hypersensitivity, delayed gastric emptying, impaired gastric fundus accommodation, Helicobacter pylori infection and psychosocial factors. Recent work suggests that NERD is also a heterogeneous disorder, with some demonstrating abnormal acid exposure and/or sensitivity and others entirely normal 24-h pH studies (functional heartburn). It would appear that the overlap of these two conditions is most apparent between FD and those NERD patients with normal pH studies.