It is clear that non-ulcer (or functional) dyspepsia is a heterogeneous syndrome that includes a subset of patients with unrecognized gastroesophageal reflux. Patient heterogeneity combined with inadequate study methodology has led to enormous confusion in interpreting the relationship between Helicobacter pylori and non-ulcer dyspepsia. The possibility that H. pylori is associated with gastroesophageal reflux disease may explain, in part, the difficulty in establishing a link between non-ulcer dyspepsia and H. pylori infection. It is unclear whether the prevalence of H. pylori is increased in non-ulcer dyspepsia over and above the background population. H. pylori does not appear to be linked to heartburn or other specific upper gastrointestinal tract symptoms. The results of eradication trials in H. pylori-infected patients with non-ulcer dyspepsia have been equivocal and generally flawed. There is no doubt that H. pylori is not a sufficient cause of non-ulcer dyspepsia, because it is well documented in the literature that dyspepsia can occur in the absence of infection and infection can occur in the absence of symptoms. At this stage, there is insufficient evidence to support the hypothesis that H. pylori is etiologically linked to non-ulcer dyspepsia, but data from well designed large randomized controlled trials of eradication therapy, are awaited with great interest.