Objective To investigate the alteration of serum ghrelin and leptin in patients with functional dyspepsia (FD) and their clinical significance. Methods Sixty patients with FD [-30 patients with postprandial distress syndrome(PDS) and 30 patinets with epigastric pain syndrome(EPS)] were enrolled. Thirty healthy subjects were severed as controls. The serum ghrelin and leptin were measured by enzyme linked immunosorbent assay and radioimmunosorbent assay, respectively. Results The concentrations of serum ghrelin and leptin were both significantly lower in patients with FD than in controls (P<0.01). Meanwhile, the concentrations of serum ghrelin and leptin in PDS patients were significantly lower compared with controls (P<0.01) and EPS patients (P<0.01). There was no significant difference in levels of serum ghrelin and leptin between controls and EPS patients(P>0.05). Conclusions The alterations of serum ghrelin and leptin in PDS patients are responsible for their reduction in FD patients. The PDS may he associated with abnormalities in gastrointestinal motility. There is an interaction between serum ghrelin and leptin in development of FD. The detection of serum ghrelin or leptin is helpful in classification and treatment of FD.