In zebra finches, estrogen is a potent hormone that masculinizes the neural circuitry controlling song during development and activates song in adulthood. However, previous studies have reported conflicting patterns of estrogen receptor (ER) expression in the song control regions. To obtain additional information about the distribution of ER in the zebra finch brain, a cDNA encoding an estrogen receptor was isolated from a zebra finch hypothalamic-preoptic area cDNA library. The 2792 bp insert contains a 1764 bp open reading frame with 5' and 3' untranslated regions of 132 bp and 896 bp, respectively. The deduced polypeptide is 589 amino acids in length and is highly homologous to the estrogen receptors of chicken (97%), rat (79%), mouse (79%), human (78%), Xenopus laevis (76%) and trout (49%). Northern blot analysis revealed three ER mRNAs expressed differentially in ovary, oviduct and telencephalon. The smallest transcript, 4.1 kb, was expressed in all three tissues, whereas larger mRNAs were expressed in ovary (7.6 kb) and oviduct (8.1 kb). In situ hybridization histochemistry revealed strong labelling in the infundibular region of the hypothalamus, preoptic area, and medial caudal neostriatum. Few or no labelled cells were found in the song control nuclei (HVC, RA, MAN or Area X). These results are consistent with previous studies that have shown ER protein and binding in hypothalamic and preoptic area and a lack of ER in most regions that control song production.