Introduction: The mitochondrial uncoupling proteins (UCPs) constitute a unique group of closely related proteins that are known to be involved in thermogenesis and may play important roles in suppression of reactive oxygen species (ROS) formation and fatty acid metabolism. Although a role for UCP1 in thermogenesis in unerring, the physiological functions of UCP2 and UCP3 are at present not fully understood. Synthetic agonists for the peroxisome proliferator-activated receptors (PPARs) as well as fatty acids have been shown to increase murine UCP2 and UCP3 mRNA expression but response elements and mechanisms are not yet characterized. The aim of this study was to investigate the transcriptional regulation of UCP3 by the PPARs. Results: The PPAR agonists increase UCP2 and UCP3 mRNA expression in skeletal muscle cells (C2C12). In addition, UCP2 and UCP3 mRNA expression is upregulated during 3T3-L1 adipocyte differentiation. Results from sequencing of chromatin immunoprecipitated (ChIP) material from 3T3-L1 adipocytes revealed three PPAR and retinoid X receptor (RXR) binding sites in and around the murine UCP3 gene. The recruitment of PPAR and RXR to the three potential PPREs was determined by ChIP combined with quantitative PCR in 3T3-L1 cells during adipocyte differentiation, in mouse liver, in mouse skeletal muscle, and in murine myoblast skeletal muscle cells (C2C12). The results show that RXR and PPAR are recruited to three putative PPREs at -11250, -7000, and +1750 relative to the UCP3 transcriptional start site, respectively. Interestingly, the relative occupancy appears to be cell type specific.