The sexual differentiation of the brain is orchestrated by gonadal steroids during a restricted developmental period and results in permanent changes in the neural substrate including the capacity to support ovulation and expression of sex-specific reproductive behaviors. Sry gene-induced development of testes constitutes a binary switch directing all subsequent differentiation. Androgen produced by the testes of the embryonic male differentiates secondary sex characteristics but also acts in the brain to "masculinize" the neural substrate, many of the latter are the result of aromatization of testosterone to estrogen. Molecular characteristics of aromatase and 5 alpha-reductase enzymes are reviewed. It is assumed that estrogen binds to its receptor which then binds to DNA, inducing transcription of specific genes. Mutations in steroid receptor genes can markedly alter hormone-mediated differentiation. Two questions are addressed: (1), is the assumption correct that estrogen's effects on sexual differentiation are via the classic genomic action of steroids?; and (2) if so, what genes are transcribed as a result of the activated estrogen receptor complex? We have used antisense oligodeoxynucleotides designed to hybridize with and block the translation of mRNA for the estrogen receptor. Administration of antisense into brain of 3-day-old pups had permanent effects on estrogen-induced differentiation as indicated by behavioral and brain morphology differences in adulthood. These results demonstrate the effectiveness of antisense oligonucleotides if administered during a critical period and further confirm the widely accepted tenet that estrogen acts on the brain via its receptor. Subsequent experiments can now address the question of what genes are being activated by the estrogen receptor during development.