Hepatocyte nuclear factor-6 (HNF-6) is the ONECUT-homeodomain transcription factor that is enriched in liver and also present in pancreas and central nervous system. It is expressed in the pancreatic bud at E10.5. In adult pancreas, its expression is restricted to the exocrine pancreas and duct cells. Since duct cells are thought to be precursors of endocrine cells and HNF-6 is involved in the regulation of the expression of HNF-4alpha and -1beta, genes that cause maturity onset diabetes of the young (MODY), we hypothesized that the sustained expression of HNF-6 would affect beta-cell function. We generated transgenic mice over-expressing human HNF-6 using the mouse insulin I promoter (MIP). We obtained one female founder in which the transgene had been incorporated into two sites; the chromosome (Ch) 14 and the X chromosome. The integration site of the latter was within centromeric heterochromatin and the transgene was inactivated. Studies on mice in which the transgene was integrated into Ch14 showed beta-cell specific defects functionally and pathologically. The insulin secretory response to glucose and arginine in the in situ-perfused pancreas was also significantly impaired in these mice. Immunohistochemical analysis revealed that the islets were smaller and had an abnormal architecture with an inverted ratio of alpha- and beta-cells resulting from beta-cell loss to 30% by 6-wk of age. The decreased number of beta-cells was quantified first time by fluorescent activated cell sorting using entire pancreata from the transgenic mice crossed with MIP-green fluorescent protein (GFP) mice. This severe loss of beta-cells involved programmed cell death.