We have identified several estrogen receptor (ER) mRNA isoforms in rat pituitary and characterized their regulation by gonadal steroids. The ER mRNAs correspond to splice variants in which either exon 4, exons 3 and 4, or exons 5 and 6 are deleted. A previously isolated pituitary-specific truncated mRNA, TERP-1, containing a unique 5'-end and exons 5 through 8 of the full-length ER, was also studied. The exon deletion variants were expressed in males and females, in pituitary, uterus, testes, heart, hypothalamus, and liver. An antibody to the ER C-terminus bound to full-length (64 kDa) and smaller (50 55 kDa and 40-45 kDa) ER proteins in uterus and pituitary and a pituitary-specific ER of 20-24 kDa corresponding to TERP-1. Estrogen (E) treatment in vivo stimulated full-length ER 2-3-fold, and TERP-1 7-10-fold, but had no effect on any exon deletion variant. Progesterone treatment, alone or with E, had no consistent effect on any ER mRNA form. TERP-1 mRNA was also dramatically and specifically modulated during the estrous cycle, increasing approximately 500-fold between the morning of diestrous and the afternoon of proestrus. Thus, ER mRNA variants exist in estrogen-responsive tissues; the pituitary contains at least one tissue-specific ER which is regulated by steroids and which may contribute to changes in regulated biological activity.