This study investigated the metabolism of 5-FU and deoxyuridine in rat brain mitochondria, which has implications for glioma treatment. The key findings were: 1) 5-FU is phosphorylated to 5-FUTP in brain mitochondria, which can cause RNA incorporation but does not compete with or reduce TTP pools. 2) dUTP levels are regulated by a highly active dUTPase enzyme to limit incorporation into mtDNA through futile cycling of dUMP and dUTP. 3) There is no evidence of thymidine phosphorylase or thymidylate synthase activity, suggesting brain mitochondria rely on salvage pathways for dNTP pools.