Ligation of the pancreatic duct has been shown to induce islet cell neogenesis from duct cells in the adult rat pancreas. The transcription factors that regulate islet cell neogenesis and the phenotype of putative precursor cells involved in neogenesis are unknown. We, therefore, studied the expression of the transcription factors Pdx1, Pbx1, Meis2, Nkx2.2 and the putative stem cell markers c-Kit and nestin in rat pancreata 3, 5 and 7 days after duct ligation. Immunocytochemical staining revealed a subpopulation of cells in the ligated portion of the pancreas that was positive for the putative stem cell markers c-Kit and nestin. The c-Kit immunoreactivity was upregulated, reaching a peak at day 3, while nestin expression peaked at day 7. The c-Kit-positive cells were located among the duct and islet cells, while nestin-expressing cells were found scattered in the duct epithelium at day 3 and around the ducts at day 7. Both c-Kit- and nestin-positive cells showed high proliferative activity, as determined by BrdU labeling. Pdx1 and Nkx2.2 were found predominantly in the duct cells of the ligated pancreas. There were significant changes in the expression patterns of Pbx1 and Meis2 in the ductular complexes. The findings indicate that the stem cell markers c-Kit and nestin as well as the transcription factors Pdx1 and Nkx2.2 are upregulated in compartments of the pancreas that are involved in islet cell neogenesis after duct ligation.