Background and Aim: Delayed gastric emptying is one of the reasons why functional dyspepsia (FD) occurs. The 13C-acetate breath test is widely used to evaluate gastric emptying. Nevertheless, the standard value of 13C-acetate breath test has not taken into account the gender difference of gastric emptying among healthy individuals. The main aim of this study was to readjust the standard value of 13C-acetate breath test in the light of gender differences. In addition, we clarified the prevalence and clinical characteristics of delayed gastric emptying in patients with FD using the modified standard values of 13C-acetate breath test. Methods: Fifty-two healthy individuals and 126 patients with patients with FD were enrolled. Gastric emptying was evaluated by the 13C-acetate breath test. The cut-off points of Tmax for the diagnosis of delayed gastric emptying were determined on the basis of results from healthy individuals making a distinction of genders. Gastroesophageal reflux symptoms, dyspeptic symptoms, scores of anxiety and depression, age, body mass index (BMI), smoking and alcohol consumption were compared between the delayed gastric emptying group and the non-delayed gastric emptying group. Results: Since gastric emptying was delayed in healthy women compared with that in healthy men (Tmax, 53.6 ± 19.3 vs. 42.7 ± 16.9 min, p = 0.04), we set the cut-off points of Tmax at 60 min in men and at 75 min in women. In patients with FD, the prevalence of delayed gastric emptying was not different between men and women with the modified standard values of 13C-acetate breath test. (31.0 vs. 27.4%, p = 0.68). BMI was lower in the delayed gastric emptying group than in the non-delayed group among the male patients. Reflux symptoms were more severe in delayed gastric emptying group than in the non-delayed group among the female patients. Conclusion: The standard values of 13C-acetate breath test should be modified bearing the gender difference in mind. It provides us more appropriate information to understand the mechanisms of FD.