Thiamine, in its diphosphate form, is a required cofactor for enzymes of glucose metabolism and branched-chain alpha-ketoacid dehydrogenase (BCKDH). Although metabolic impairments in glucose metabolism have been found to occur in selectively vulnerable brain regions of the thiamine-deficient (TD) brain, the effects of thiamine deficiency on BCKDH have not been studied. BCKDH activity was assayed radiochemically in brain extracts of vulnerable (medial thalamus; MT) versus non-vulnerable (frontal cortex; FC) brain regions of rats made TD by administration of the central thiamine antagonist, pyrithiamine. A significant regional variation in BCKDH within the TD rat brain was noted, with a higher capacity for branched-chain amino acid oxidation in FC compared to MT: BCKDH activity was significantly reduced in MT of TD rats, resulting in selective accumulation of BCAAs in this brain region. Leucine concentrations were elevated over fivefold in the MT of symptomatic TD rats, compared with pair-fed control (PFC) rats. Impaired branched-chain ketoacid metabolism in rats may contribute to the neuronal dysfunction and ultimate thalamic neuronal cell death observed in thiamine deficiency.