Pancreatic ␣ and  cells are derived from the same progenitors but play opposing roles in the control of glucose homeostasis. Disturbances in their function are associated with diabetes mellitus. To identify many of the proteins that define their unique pathways of differentiation and functional features, we have analyzed patterns of gene expression in ␣TC1.6 vs. MIN6 cell lines by using oligonucleotide microarrays. Approximately 9 -10% of >11,000 transcripts examined showed significant differences between the two cell types. Of >700 known transcripts enriched in either cell type, transcription factors and their regulators (TFR) was one of the most significantly different categories. Ninety-six members of the basic zipper, basic helix-loop-helix, homeodomain, zinc finger, high mobility group, and other transcription factor families were enriched in ␣ cells; in contrast, homeodomain proteins accounted for 51% of a total of 45 TFRs enriched in  cells. Our analysis thus highlights fundamental differences in expression of TFR subtypes within these functionally distinct islet cell types. Interestingly, the ␣ cells appear to express a large proportion of factors associated with progenitor or stem-type cells, perhaps reflecting their earlier appearance during pancreatic development. The implications of these findings for a better understanding of ␣ and  cell dysfunction in diabetes mellitus are also considered. P ancreatic islets consist of four endocrine cell types, ␣, , D, and pancreatic peptide (PP). These cell types produce and secrete the major islet hormones: glucagon, insulin, islet amyloid polypeptide (IAPP), somatostatin, and PP, respectively, which regulate fuel and energy homeostasis (1). The ␣ cells secrete glucagon, which stimulates gluconeogenesis and glycogenolysis to prevent hypoglycemia, whereas the  cells increase insulin secretion in response to elevated blood glucose levels. Glucagon and insulin antagonistically regulate the balance of glucose storage, production, and consumption to maintain physiological plasma glucose concentrations. Therefore, the ␣ and  cells together play a central role in glucose homeostasis.Excessive production and secretion of glucagon by the ␣ cells is a common accompaniment to the two main types of diabetes. Physiologically, glucagon secretion is suppressed by hyperglycemia. However, this normal homeostatic suppression is lost in diabetic states, which in turn perpetuates hyperglycemia by stimulating hepatic glucose output (2). Another major typical manifestation of diabetes is an absolute or relative deficiency of insulin from the  cells, resulting in failure to adequately control the blood glucose level (3). Disturbances of ␣ and͞or  cell function thus are central to the failure to maintain physiological glucose levels and related metabolic concomitants of diabetes mellitus.To understand the molecular basis for the development and specialized functions of ␣ and  cells is an important goal for understanding and effectively treating diabetes. Although much effort h...