The brain metabolites were studied in the neonatal hypothyroid rat brain using 31P and 1H nuclear magnetic resonance (NMR) spectroscopy. In vivo 31P spectroscopy of the brains in hypothyroid rats showed the tendency of decrease in phosphocreatine/Pi and phosphocreatine/ATP ratio, suggesting suppressed brain energy status. On proton analysis using perchloric acid extracts of the brain, 10 metabolites were easily recognized. Quantitative analysis of individual metabolites revealed decreased contents of GABA, NAA (N-acetyl aspartate) and phosphocreatine and increased contents of taurine in hypothyroid rat. It was concluded that NMR is a useful and promising tool to evaluate brain metabolites.