Although tissue-specific expression of the alpha1 and beta1 thyroid hormone receptors (TR-alpha1 and TR-beta1) suggests isoform-specific function, transfection studies to date have failed to show consistent differences in their ability to regulate gene expression. We here provide evidence that TR-beta1 but not TR-alpha1 regulates the expression of the gene coding for PCP-2 in cerebellar Purkinje cells during neonatal rat development and that such regulation appears to be both T3 dependent and T3 independent. Examination of neonatal rats revealed that the levels of three mRNAs expressed in cerebellar Purkinje cells (myoinositol-1,4,5-triphosphate receptor, calbindin, and PCP-2) rise from neonatal day 1 to day 15. This rise is preceded by the previously documented surge in brain T3 and TR-beta1. Methimazole-induced hypothyroidism sharply reduces, but does not abolish, the rise in these mRNAs. Concomitant T3 administration normalizes the process. In order to establish more directly the role of TR-beta1 and T3, cotransfection experiments were performed in CHO cells with PCP-2-lacZ construct and TR isoforms. These studies showed that TR-beta1, even in the absence of T3, regulated the expression of the transfected PCP-2 construct. T3 augments the response to TR-beta1 alone by 40% (P < .01). TR-alpha1 had no effect on PCP-2-lacZ expression either in the presence or absence of T3. Transfection studies using a heterologous promoter and a 205-base pair region of the PCP-2 gene showed that TR-beta1 isoform specificity resides within an upstream element of the PCP-2 gene. These studies support the hypothesis that the neonatal rise in TR-beta1 plays a crucial role in brain development.