OBJECTIVE Helicobacter pylori infection has been implicated in atrophic gastritis and gastric ulcer disease. However, the relationship between gastric emptying and Helicobacter pylori infection is still unclear. METHODS One hundred and two consecutive patients with functional dyspepsia were enrolled in this study (53 Helicobacter pylori positive and 49 negative). Gastric emptying was determined using both the 13C-octanoic acid breath test and the paracetamol absorption test. For grading gastric atrophy, the biopsy samples and serum pepsinogen I/II ratio were used. The relationship between gastric emptying, Helicobacter pylori infection and atrophy grade was investigated. RESULTS There was no significant difference in all gastric emptying parameters between Helicobacter pylori positive and negative patients. However, in Helicobacter pylori positive subjects, pepsinogen I/II ratio correlated with atrophy grade, and it also correlated with all parameters of gastric emptying. Especially in the half-emptying time, an important parameter, there was significant correlation with the pepsinogen I/II ratio (R = -0.39, p < 0.01). This finding implies that gastric emptying is delayed according to the degree of gastric atrophy. CONCLUSIONS Gastric emptying was not delayed simply according to advanced age, but according to the advance in gastric atrophy.