Estrogen regulates diverse physiological processes by acting through receptors, two major forms of which have been identified: estrogen receptors alpha (ERa) and beta (ERb). The existence of two subtypes may partly explain the selective actions of estrogen in different target tissues and in the same tissue during different physiological states. Although the cellular distribution of ERa and ERb had been demonstrated before in the reproductive organs there was a lack of a comprehensive map of ER in the reproductive organs from development through adulthood, and in some cases, there was complete lack of information on some parts of the organs, notably the penis. This study provides a comprehensive cellular distribution map of the two ER subtypes, ERa and ERb mRNAs, for the entire reproductive organs of the male and female rat from development through adulthood using various techniques, notably in situ hybridization, and in some cases PCR (semi-quantitative PCR and qPCR), Western Blot analysis and confocal immunofluorescence. This was the first study to demonstrate the presence of ER in the penis.