We report the identification of a novel cDNA fragment that shows significantly reduced expression in cancerous tissue compared with paired non-cancerous liver tissue in patients with hepatocellular carcinoma (HCC). The full-length transcript of 1733 bp encodes a protein of 308 amino acids that has all the hallmark features of mitochondrial carrier proteins. We designate the novel protein as HDMCP (HCC-down-regulated mitochondrial carrier protein). The HDMCP orthologs in human, mouse, and rat are found to exhibit close similarity in protein sequence and gene organization, as well as exclusive expression in the liver. Moreover, conserved syntenic regions have been demonstrated at the HDMCP gene locus in the human, mouse, and rat genome. Taken together, we suggest that HDMCP might have a conserved and unique biological function in the liver. Overexpression of HDMCP in transiently transfected cancer cells results in the loss of staining by MitoTracker dye, indicating that HDMCP could induce the dissipation of mitochondrial membrane potential (DeltaPsim). However, HDMCP-mediated disruption of DeltaPsim is not related to mitochondrial permeability transition or apoptosis. In addition, we further demonstrate that the dissipation of DeltaPsim is accompanied by significant reduction of cellular ATP in 293T cells overexpressing HDMCP or uncoupling protein 2 (UCP2). Our present findings suggest that HDMCP might be one of the long postulated uncoupling proteins that catalyze the physiological "proton leak" in the liver. The down-regulation of HDMCP in HCC cancer cells might result in the elevation of DeltaPsim, a common phenomenon found in cancer cells.