Metabolic pathway mapping using 13C NMR spectroscopy has been used extensively to study interactions between neurons and glia in the brain. Established extraction procedures of brain tissue are time consuming and may result in degradation of labile substances. We examined the potential of mapping 13C-enriched compounds in intact brain tissue using high-resolution magic angle spinning (HR-MAS) NMR spectroscopy. Sprague–Dawley rats received an intraperitoneal injection of [1,6-13C]glucose, and 15 min later the animals were subjected to microwave fixation of the brain. Quantification of concentration and 13C labelling of metabolites in intact rat thalamus were carried out based on exogenous ethylene glycol concentrations measured from 1H NMR spectra using an ERETIC (Electronic REference To access In vivo Concentrations) signal. The results from intact tissue were compared with those from perchloric acid-extracted brain tissue. Amounts of 13C labelling at different positions (C2, C3 and C4) in glutamate, glutamine, γ-aminobutyric acid and aspartate measured in either intact tissue or perchloric acid extracts were not significantly different. Proton NMR spectra were used for quantification of six different amino acids plus lactate, inositol, N-acetylaspartate, creatine and phosphocreatine. Again, results were very similar when comparing the methods. To our knowledge, this is the first time quantitative 13C NMR spectroscopy measurements have been carried out on intact brain tissue ex vivo using the HR-MAS technique. The results show that HR-MAS 13C NMR spectroscopy in combination with 1H NMR spectroscopy and the ERETIC method is useful for metabolic studies of intact brain tissue ex vivo. Copyright © 2008 John Wiley & Sons, Ltd.