Background: Glutaryl-CoA dehydrogenase deficiency is an inborn error of lysine metabolism. Patients are characterized by neurodegeneration affecting basal ganglia induced by glutaric and 3-OH-glutaric acid accumulation. The precise pathway of lysine degradation and its subcellular localization is unclear. It is thought that there is a main, mitochondrial and a minor, peroxisomal pathway. We studied the individual steps of both pathways in Gcdh-deficient mice and potential therapeutic aspects of their modification. Methods: We tested activities and localization of saccharopine dehydrogenase, aminoadipate semialdehyde dehydrogenase, aminoadipate transaminase, 2-oxoadipate dehydrogenase, and pipecolate oxidase in liver, brain, and kidney. Further, we induced peroxisomal biogenesis by clofibrate and examined its effect on production of glutaric and 3-OH-glutaric acid.