Intestinal stem cells (ISCs) in the Drosophila midgut have emerged as an excellent model for the study of epithelial stem cells and homeostasis. The modes of ISC fate, their ability to respond to tissue damage and the signaling pathways involved in their regulation are broadly conserved with mammalian epithelia of the intestine, epidermis and esophagus. While the extrinsic signaling pathways regulating Drosophila ISCs have been extensively studied over the last several years, less is known about the intrinsic determinants of stem cell fate. We have used targeted DamID to profile gene expression in undisturbed stem/progenitor cells and the major differentiated cell type (enterocytes). This allowed us to identify 53 transcription factors specifically expressed or enriched in the stem/progenitor population. Characterization of the most highly enriched TFs identified critical regulators of proliferation and differentiation with mammalian orthologs implicated in epithelial homeostasis or cancer. Target profiling by DamID reveals binding to the regulatory regions of cell cycle genes and signaling pathway components, providing possible links between intrinsic and extrinsic regulators of ISC fate.