Mechanism of thymic compartmentalization was studied in the transgenic system using the promoter of thymic stromal cotransporter (TSCOT), a cortical thymic epithelium-specific gene. The transgenic 3.1 kb TSCOT (3.1T) and 4.4 kb TSCOT (4.4T) promoters recapitulated the thymic organ and the cortical epithelial cell-specific expression at the newborn stage. However, the 3.1T driving enhanced green fluorescent protein (EGFP; 3.1T-EGFP) or Cre-recombinase (3.1T-CreE) redistributed the expression into the medulla at the adult stages. Two Cre-transgenic lines (3.1T-CreE and 4.4T-CreE), when crossed with the ROSA LacZ or EGFP lines, showed the reporter expression in both the cortex and the medulla. TSCOT promoter activities were also verified in the transient thymic epithelial cell (TEC) population expressing keratin 5 and keratin 8. These indicate that the TSCOT promoter is turned on in the bipotent TEC precursors and regulated in a compartment-specific, developmentally regulated fashion. These transgenic lines provide the useful systems for delineating the specific pathways for TEC lineage development and function.