The mitochondrial carnitine system catalyzes the transport of long-chain fatty acids into the mitochondrial matrix where they undergo beta oxidation. This transport system consists of the malonyl-CoA sensitive carnitine palmitoyltransferase I (CPT-I) localized in the mitochondrial outer membrane, the carnitine:acylcarnitine translocase, an integral inner membrane protein, and carnitine palmitoyltransferase II localized on the matrix side of the inner membrane. (Kerner & Hoppel, 2000; Ramsay et al. 2001). Additional reactions annotated here enable the uptake of carnitine and the regulation of fatty acid biosynthesis at the level of ACACA and ACACB to minimize simultaeous mitochondrial catabolism and cytosolic biosynthesis of long-chain fatty acids.