The tumor necrosis factor receptor-associated protein 1 (TRAP-1) interacts with a variety of proteins involved in diverse functions. We have used quantitative immunogold electron microscopy and biochemical analysis to evaluate the subcellular distribution of TRAP-1 in rat tissues. Immunofluorescence employing a polyclonal antibody raised to human recombinant TRAP-1 reveals specific staining of mitochondria and nuclear region in mammalian cells. Western blot analysis of purified rat liver mitochondrial subfractions with the TRAP-1 antibody reveals that the cross-reactive protein (M(r) approximately 80 kDa) is mainly present in the matrix compartment. Immunogold labeling of rat tissue sections embedded in LR Gold resin shows strong labeling of mitochondria in all the tissues examined (viz., liver, heart, pancreas, kidney, spleen, anterior pituitary gland). Additionally, specific and significant labeling with TRAP-1 antibody was also observed in certain tissues in a number of nonmitochondrial locations, including pancreatic zymogen granules, insulin secretory granules, cardiac sarcomeres, and nuclei of pancreatic and heart cells, and on the cell surface of blood vessel endothelial cells. Western blot analysis showed that a cross-reactive protein of similar molecular mass as TRAP-1 is present in purified pancreatic zymogen granules. Immunogold labeling was prevented in all tissues by preadsorption of the TRAP-1 antibody with the purified recombinant TRAP-1 protein. These observations and the fact that TRAP-1 is synthesized with a typical mitochondrial targeting presequence strongly indicate that TRAP-1 is primarily a mitochondrial matrix protein. The localization of this protein at specific extramitochondrial sites raises interesting and fundamental questions regarding the possible mechanisms by which these proteins are translocated to such sites. Copyright 2000 Academic Press.