Mitochondrial uncoupling proteins (UCPs) have been postulated to be regulators of thermogenesis, energy balance, and oxidative stress. Brain mitochondrial carrier protein-1 (BMCP1) is a new member of the UCP family, but little is known about the gene regulation and the role of BMCP1 in the central nervous system. In the present study, we first cloned BMCP1 cDNA encoding 325 amino acids from rat brain. The BMCP1 mRNA showed a distinct distribution pattern compared with that of UCP2 gene in human brain. Cold exposure did not affect the mRNA levels of BMCP1 and UCP2 in rat whole brain, but did increase the expression of UCP2 in the spinal cord. The mRNA level of BMCP1 in the brain of 26-month-old rats was decreased by 30% and that of UCP2 increased by 60% compared with the levels in 6-month-old rats. These results suggest differential roles of BMCP1 and UCP2 in thermoregulation and aging.