Thyroid hormone (tri-iodo-thyronine, T3) exerts transcriptional effects on target genes in responsive cells. These effects are determined by DNA/protein interactions governed by the type of T3 receptors (TRs) in the cell. As TRs show tissue and developmental variations, regulation is best addressed in an integrated in vivo model. We examined TR subtype effects on thyrotropin-releasing hormone (TRH) transcription and on the pituitary/thyroid axis end point: thyroid hormone secretion. Polyethylenimine served to transfect a TRH-luciferase construct containing 554 bp of the rat TRH promoter into the hypothalami of newborn mice. Transcription from the TRH promoter was regulated in a physiologically faithful manner, being significantly increased in hypothyroidism and decreased in T3-treated animals. Moreover, when various ligand binding forms of mouse or chicken TRbeta and TRalpha were expressed with TRH-luciferase, all forms of TRbeta gave T3-dependent regulation of TRH transcription, whereas transcription was T3 insensitive with each TRalpha tested. Moreover, chicken TRalpha increased TRH transcription sixfold, whereas mouse TRalpha decreased transcription. These transcriptional effects had correlated physiological consequences: expression of the chicken TRalpha in the hypothalamus of newborn mice raised circulating T4 levels by fourfold, whereas mouse TRalpha had opposite effects. Thus, TR subtypes have distinct, physiologically relevant effects on TRH transcription.