The postnatal development of the epididymis is a complex and poorly understood process. Our recent studies have shown that undifferentiated primitive small columnar cells are stem cells and can differentiate in vitro into basal and principal cells. This process represents a key aspect of early epididymal development. As such, the genes and signaling pathways implicated in the differentiation of stem cells are critical. In the rat, epididymal development has been subdivided into three phases consisting of an undifferentiated epithelium (birth to day 14), differentiation (days 14 to 44), and expansion (day 45 to adult). During this period, changes in gene expression in the epididymis are the most significant, as almost 1500 genes are differentially expressed between epididymides of 7 and 18 days of age. In the adult rat, basal cells appear to represent a quiescent adult stem cell population that can be cultured under 3D conditions and can differentiate into principal cells. Gene expression in basal cells of adults compared with epididymides from day 7 rats reveals approximately 400 genes that are common to both. Analyses of these genes predict multiple signaling pathways and master regulator genes. Their roles in early epididymal development suggest that the process is complex and involves multiple regulators, cell surface factors, signaling pathways, and hormones that are interconnected and which promote the differentiation of epididymal basal cells into other epididymal cell types.