Our earlier studies showed that estrogen was involved in the regulation of fluid reabsorption in adult mouse efferent ductules (ED), through estrogen receptor (ER) α and ERβ, by modulating gene expression of epithelial genes involved in ion homeostasis. However, little is known about the importance of ERα in the ED during postnatal development. Based on previous findings, we hypothesized that there should be a difference in the expression of epithelial ion transporters and anion producers in the ED of postnatal wild type (WT) and estrogen receptor α knockout (αERKO) mice. Using absolute, comparative and semi-quantitative RT-PCR along with immunohistochemistry, we looked at expression levels of several genes in the ED across postnatal development. The presence of estrogen in the testicular fluid was indirectly ascertained by immunohistochemical detection of the P450 aromatase in the testis. There was no immunohistochemically detectable difference in the expression of P450 aromatase in the testes and ERβ in the ED of WT and αERKO mice. ERα was only detected in the ED of WT mice. The absence of ERα in the ED of postnatally developing mice resulted in differential expression of mRNAs and/or proteins for carbonic anhydrase II, Na + /H + exchanger 3, down-regulated in adenoma, cystic fibrosis transmembrane regulator, and Na + /K + ATPase α1. Our data indicate that the absence of ERα resulted in altered expression of an epithelial ion producer and transporters during postnatal development of mice. We conclude that the presence of ERα is important for regulation of the ED function during the prepubertal developmental and postpubertal period.