In rat liver, comparisons of marker enzyme activities (beta-hexosaminidase, lysosomes; catalase, peroxisomes; cytochrome oxidase, mitochondrial-inner membrane; monoamine oxidase, mitochondrial outer membrane; ornithine aminotransferase, mitochondrial matrix) show that lysine-alpha-ketoglutarate reductase and saccharopine dehydrogenase, the initial enzymes of saccharopine-dependent lysine degradation, are found only in the mitochondrial matrix. These results are consistent with obligatory uptake of lysine into the matrix for lysine catabolism and raise the possibility that lysine transport into the mitochondrion may control lysine degradation.