The epididymis is divided into caput, corpus and cauda regions, organized into intraregional segments separated by connective tissue septa (CTS). In the adult rat and mouse these segments are highly differentiated. Regulation of these segments is by endocrine, lumicrine and paracrine factors, the relative importance of which remains under investigation. Here, the ability of the CTS to limit signaling in the interstitial compartment is reviewed as is the effect of 15 days of unilateral efferent duct ligation (EDL) on ipsilateral segmental transcriptional profiles. Inter-segmental microperifusions of epidermal growth factor (EGF), vascular endothelial growth factor (VEGFA) and fibroblast growth factor 2 (FGF2) increased phosphorylation of mitogen activated protein kinase (MAPK) in segments 1 and 2 of the rat epididymis and the effects of all factors were limited by the CTS separating the segments. Microarray analysis of segmental gene expression determined the effect of 15 days of unilateral EDL on the transcriptome-wide gene expression of rat segments 1-4. Over 11 000 genes were expressed in each of the four segments and over 2 000 transcripts in segment 1 responded to deprivation of testicular lumicrine factors. Segments 1 and 2 of control tissues were the most transcriptionally different and EDL had its greatest effects there. In the absence of lumicrine factors, all four segments regressed to a transcriptionally undifferentiated state, consistent with the less differentiated histology. Deprivation of lumicrine factors could stimulate an individual gene\'s expression in some segments yet suppress it in others. Such results reveal a higher complexity of the regulation of rat epididymal segments than that is generally appreciated.