The transcription factor paired-box-6 (Pax6) plays a key role in the endocrine differentiation cascade of the pancreas. Mutations in Pax6 are associated with anomalies including diabetes. This study elucidates the impact of Pax6 in pancreatic a- and ß-cell function and differentiation. In a-cells, we found Pax6 to be critical for glucagon biosynthesis and processing, by directly and indirectly activating the glucagon gene through the transcription factors cMaf and NeuroD1, and the processing enzyme of proglucagon in a-cells PC2 and its molecular chaperon 7B2. In regard to ß-cells, the study foundsPax6 to control the cell function and differentiation through the control of genes coding for insulin-1, insulin-2, glucose-transporter-2, glucokinase, GLP-1-receptor, FFA receptor GPR40 as well as the transcription factors Pdx1, MafA and Nkx6-1. The study maps the complex network in which Pax6 regulates transcription of genes important for differentiation of the endocrine pancreas and plays a major role in the islet function.