Patients with Helicobacter pylori (H. pylori) infection may complain of dyspeptic symptoms without presence of macroscopic lesions on gastroduodenal mucosa. Such a condition is usually recognized as functional dyspepsia, and different pathogenetic mechanisms are involved. The role of H. pylori in these patients is controversial. Several trials assessed the potential role of H. pylori eradication in improving dyspeptic symptoms, and data of some meta-analyses demonstrated that cure of infection is associated with a small (10%), but significant therapeutic gain as compared to placebo. The reason for which dyspeptic symptoms regress in some patients following bacterial eradication, but persist in others remains unclear. Regrettably, trials included in the meta-analyses are somewhat different for study design, definition of symptoms, assessment of symptoms changes, and some may be flawed by potential pitfalls. Consequently, the information could be not consistent. We critically reviewed the main available trials, attempting to address future research in this field.