The effects of bacterial endotoxin (lipopolysaccharide; LPS) on the cerebral blood flow (CBF), amino acid levels and brain histology were studied in young rabbits. The CBF was slightly decreased in the cerebral cortex and markedly decreased in the cerebral white matter at 60 and 120 min after LPS administration. Histological examination revealed only slightly pyknotic neurons around small vessels at 24 hours, and multifocal necrosis in the deep cerebral cortex and white matter at 72 hours. Some amino acids were increased in the plasma and brain regions at 24 hours after LPS administration, most of which were essential amino acids. GABA in the cerebral white matter was decreased at 24 hours. At 72 hours, most non-essential and glucogenic amino acids were decreased. These results suggest that the brain histological changes are related mainly to hypoperfusion and vascular damage in the brain. The amino acid changes may also be related to inappropriate amino acid metabolism associated with brain cell damage.