Rat brown adipocytes express mRNAs for Uncoupling Proteins (UCP) 1, 2 and 3 and the Peroxisome Proliferator Activated Receptors (PPAR) alpha and gamma. We have examined the effects of selective PPAR alpha or -gamma activation on changes in UCP-1 and UCP-3 mRNA levels in cultured fetal rat brown adipocytes (FBA). Rosiglitazone (1.0 mu M), a selective PPAR gamma agonist, elicited 5- and 3-fold increases in UCP-1 and UCP-3, respectively. The PPARa ligand, Wy14643 (10.0 mu M) increased UCP-3 tenfold, but decreased UCP-1. A synergistic effect on UCP-3 expression (30-fold increase; P < 0.05) was observed when FBA were exposed to a combination of Wy14643 (10.0 mu M) and rosiglitazone (10.0 mu M). Thus, activation of PPAR gamma increases UCP-1 and UCP-3 levels which are differentially regulated by PPAR alpha. A synergistic interaction occurs between PPAR alpha and PPAR gamma in the regulation of UCP-3 in FBA, probably via co-activator recruitment, suppression of co-repressor proteins or through a direct interaction at the level of the PPRE.