The fact that male estrogen receptor alpha (ERα) knockout mice are infertile indicates a role for this receptor in male reproduction. Here, objectives were to evaluate ERα expression in male goat reproductive tissues at the transcriptional level using RNase protection assay (RPA) and in situ hybridization (ISH), and to clone a partial cDNA for caprine ERα using reverse transcription-polymerase chain reaction (RT-PCR). For RPA and ISH procedures, a radiolabeled antisense cRNA probe, generated in vitro from the ovine oER8 cDNA template, was employed. Evaluations were made on individual samples obtained from adult goats. Labeled cRNA sense probe was used as a negative control in ISH. A 530-base pair amplicon was generated by RT-PCR from efferent ductules (EDs), epididymis (EP), and testis, cloned from the ED and EP, and sequenced. The caprine ERα (cERα) cDNA displayed 81%–96% sequence identity with that of other species. A signal indicative of ERα mRNA was identified by both RT-PCR and RPA in all tissues, but was strongest in the ED. Compared with ED, ERα signal was sixfold lower in the EP, and 66-fold lower in the testis. Similarly, strong ERα expression was observed in ED epithelium, whereas little or no signal was detected in EP or testis by ISH. Thus, among different segments of the male reproductive tract and testis, the highest level of ERα mRNA expression was found in epithelium of the ED.