Thyroid hormone (TH) promotes cardiac mitochondrial maturation and substrate metabolism after birth. This regulation involves ligand-dependent binding of nuclear TH receptors to target gene elements. TH also putatively controls genes indirectly by modulating transcription and/or translation of other nuclear steroid receptors and coactivators, such as peroxisome proliferator-activated receptor-␣ (PPAR␣) and peroxisome proliferator-activated receptor-␥ coactivator-1 (PGC-1). We tested the hypothesis that TH influences PPAR␣ and PGC-1 regulation of metabolic genes during postnatal maturation in sheep heart in vivo. We measured their mRNAs and/or protein levels and downstream targets in left ventricle from lambs: fetal (F), 30-day-old after postnatal thyroidectomy (THY), and 30-day-old euthyroid (Con). Both PPAR␣ and PGC-1 mRNA expression decreased from F to Con, while PGC-1 protein increased substantially and PPAR␣ did not change. THY limited this mRNA response and attenuated the paradoxical postnatal PGC-1 protein elevation but did not alter mRNA levels for PPAR␣, nuclear respiratory factor-1 and hypoxia-inducible factor-1␣. THY promotion in PPAR␣ mRNA did not change PPAR␣ protein or mRNA for PPAR␣ target genes, pyruvate-dehydrogenase kinase 4 (PDK4) and muscle type carnitine palmitoyltransferase I (mCPTI). THY reduction in PGC-1 protein occurred, while reducing cytochrome c oxidase and cytochrome c content and decreasing cardiac maximal inherent respiratory capacity. These data imply that TH modulates mitochondrial maturation partly through posttranscriptional control of PGC-1, while any important regulation of PDK4 and mCPTI by change in PPAR␣ protein expression remains doubtful. Also, the paradoxical expression pattern between mRNA and protein, particularly for PGC-1, suggests a feedback control mechanism. carnitine palmitoyltransferase I; fatty acid metabolism; mitochondrial biogenesis THYROID HORMONE (TH) regulates mitochondrial biogenesis and energy metabolism in heart during maturation (30). Developmental regulation presumably occurs through ligand-dependent binding of TH receptors (TRs) to enhancer sequences or TH response elements (TREs) for genes involved in oxidative phosphorylation or substrate oxidation (21,26,29,34). Triiodothyronine (T 3 ), the active form of TH, serves as the primary ligand for these receptors. Ligand binding promotes recruitment of coactivators, which modulate transcriptional activity of these genes (26). However, T 3 also regulates genes containing no apparent TRE within the promoter region.(37) This phenomenon supports metabolic regulation by T 3 through intermediate factors, including transcriptional activators and coactivators. Thus TH hormone working through direct and indirect modulation of oxidative phosphorylation and substrate oxidation genes could broadly coordinate developmental modifications in energy-producing pathways during the perinatal period.Evidence for this coordination is provided by the perinatal TH surge, which coincides with a switch in myocardial substrate...