High-resolution magic angle spinning (MAS) (1)H nuclear magnetic resonance (NMR) spectroscopy is increasingly being used to monitor metabolic abnormalities within cells and intact tissues. Many toxicological insults and metabolic diseases affect subcellular organelles, particularly mitochondria. In this study high-resolution (1)H NMR spectroscopy was used to examine metabolic compartmentation between the cytosol and mitochondria in the rat heart to investigate whether biomarkers of mitochondrial dysfunction could be identified and further define the mitochondrial environment. High-resolution MAS spectra of mitochondria revealed NMR signals from lactate, alanine, taurine, choline, phosphocholine, creatine, glycine and lipids. However, spectra from mitochondrial extracts contained additional well-resolved resonances from valine, methionine, glutamine, acetoacetate, succinate, and aspartate, suggesting that a number of metabolites bound within the mitochondrial membranes occur in 'NMR invisible' environments. This effect was further investigated using diffusion-weighted measurements of water and NMR spectroscopy during state 2 and state 3 respiration. State 3 respiration caused a decrease in the resonance intensity of endogenous succinate compared with state 2 respiration, suggesting that coupled respiration may also modulate the NMR detection of metabolites within mitochondria.