Background Aims: Association between C allele of G protein β3 (GNB3) polymorphism and functional dyspepsia have been suggested. The aim of this study was to assess the role of GNB3 polymorphism as well as IL-10 and TNF-α gene polymorphisms in functional dyspepsia based on ROME III criteria in Korean. Methods: Case and control subjects of the study were recruited among Korean between December 2006 and June 2007, who visited health promotion center and digestive disease center of Konkuk university hospital for both upper and lower gastrointestinal endoscopy. All the subjects signed an informed consent for genetic analysis and completed ROME III criteria survey, questionnaire on Beck`s depressive inventory (BDI), and 36-item short Form general health survey (SF-36), Genomic DNA was extracted from leukocytes using a QIAamp blood kit (Qiagen, Germany) followed by a polymerase-chain-reaction-based method for genotyping. The presence of Hardy-Weinberg equilibrium was tested with the χ2 test for goodness of fit. Results: Genotype and allele frequencies for all polymorphisms of 50 functional dyspepsia patients and 81 normal subjects are summarized in Table 1. The GNB3 T allele was significantly related with functional dyspepsia. In addition, homogenous GNB3 825T carrier status was associated with functional dyspepsia. Neither IL-10 nor TNF-α polymorphisms were related with functional dyspepsia. Conclusions: Our study suggests that GNB3 allele frequency with T is linked to functional dyspepsia in Korean.