Objectives: The goal of this study is to averiguate whether Helicobacter pylori (Hp)-associated gastritis is involved in the etiology of functional dyspepsia (FD) or, at least in a subset of these patients. Methods: 103 consecutive FD patients were prospectively analyzed and subdivided according to their main complaints into ulcer-like FD (n = 31), dysmotility-like FD (n = 24) or nonspecific FD (n = 48). After endoscopy with gastric biopsy, gastritis and Hp infection were assessed and graded by histology according to the Sydney System. The prevalence of gastritis, Hp and disease activity were analyzed among the three FD subtypes and against 42 age, sex and race matched controls. Results: Hp was identified in 64 (62%) of the FD group and in 23 (55%) of the controls (p > 0.20, NS). We neither observed any increased prevalence of the infection among FD subgroups (dysmotility-like 58%, ulcer-like 58%, unspecified 67%), nor in the activity of gastritis among FD subgroups and controls. We conclude that Helicobacter pylori gastritis per se is not associated with functional dyspepsia.