BACKGROUND/AIMS: The pathogenesis of functional dyspepsia (FD) and irritable bowel syndrome (IBS) is considered to be multifactorial. Recently, several candidate genetic studies have suggested that serotonin transporter (SERT) gene polymorphism and G-protein beta3 (GNbeta3) C825T gene polymorphism are associated with FD and IBS. The aim of this study was to investigate SERT and GNbeta3 C825T gene polymorphism in Korean patients with functional gastrointestinal disorder (FGID) including FD and IBS. METHODS: SERT and GNbeta3 C825T gene polymorphism was assessed by polymerase chain reaction in serum samples from 62 patients with upper FGID (including 24 patients with FD) 49 patients with lower FGID (including 26 patients with IBS), and 70 healthy adults. RESULTS: There were no significant differences in the genetic polymorphism among the upper and lower FGID, FD, IBS and the control group of patients. Subtype analysis revealed that the GNbeta3 C825T C/C genotype tended to be associated with diarrhea-predominant IBS compared to the T/T genotype (p=0.049, OR= 5.333 95% CI: 1.008-28.205). CONCLUSION: SERT and GNbeta3 C825T polymorphism does not appear to be associated with FGID including FD and IBS in Koreans.