Peroxisome proliferator activated receptor (PPAR) and thyroid hormone receptor (TRs) independently regulate cardiac metabolism. Although ligands for these receptors are under evaluation for treatment of congestive heart failure (CHF), their interactions have not been investigated in heart. We tested the hypothesis that cardiac TRs interact with PPAR regulation of target genes and used mice exhibiting a cardioselective 337T TR1 mutation to reveal cross talk. This dominant negative transgene inhibits DNA binding for both wild type TR and TR. We used uncoupling protein 3 and mitochondrial thiolase esterase-1 (MTE-1) as principal reporters and analyzed gene expression from hearts of transgenic (MUT) and nontransgenic(WT) littermates 6 hours after receiving either specific PPAR ligand (WY14643) or vehicle. The interaction extent was determined using molecular arrays. In basal state, we detected no differences between groups for protein content for UCP3, PPAR, TR2, , retinoid x receptor (RXR) or peroxisome proliferator activated receptor co-activator-1 (PGC-1). However protein content for TR1, and the PPAR heterodimeric partner, RXR, were lower in MUT, while PPARincreased. We demonstrated cross-talk between PPAR and TR for multiple genes including UCP3 and MTE1. WY14643 induced a two-fold increase in UCP3 gene expression, which was totally abrogated in MUT. We showed variable cross-talk patterns indicating that multiple mechanisms operate according to individual target genes. The nonligand binding TR1 alters expression for multiple nuclear receptors providing a novel mechanism for interaction that has not been previously demonstrated. These results indicate that therapeutic response to PPAR ligands may be determined by thyroid hormone state and TR function.