BACKGROUND: Nuclear receptors are involved in the cell growth, development, differentiation, and metabolism. The orphan nuclear receptor SHP which lacks a DNA-binding domain is a negative regulator of nuclear receptor signaling pathways. In pancreas, SHP regulate transcriptional activity of HNF3 and HNF4 through binding them and BETA2 which is involved in beta cell differentiation and insulin production. Here, we examined transcriptional activity changes of genes expressed in beta cell when SHP was overexpressed. METHOD: INS-1 cells of passage number 24 - 30 were prepared. Affimetrix DNA chip was used to examine gene expression in INS-1 cell when SHP was overexpressed. INS-1 cells were infected with adenovirus-SHP to overexpress SHP. To confirm the result of DNA chip, we used real time RT-PCR. RESULT: When SHP was overexpressed by adenovirus-SHP transfection, FXR, Transforming growth factor, beta 2, fructose-1,6-bisphosphatase 2, bone morphogenetic protein 4 genes expression were increased. Contrarily, Activating transcription factor 2, Glycogen synthase kinase 3 alpha, Nur 77, fibroblast growth factor 14 genes expression were decreased. We confirmed DNA microarray analysis by real time RT-PCR. FXR, tribbles homolog 3 (Drosophila), fructose-1,6-bisphosphatase 2, CD36 genes expression were increased in real time RT-PCR. Nur 77 and cAMP response element modulator genes expression were decreased in real time RT-PCR. CONCLUSION: we identified several genes which expression are regulated by SHP in pancreas beta cell. These results help to explain how SHP act in the various metabolism of pancreas beta cell.