Magnetic resonance spectroscopy (MRS), a companion technique to the more familiar MRI scan, has emerged as a powerful technique for studying metabolism noninvasively in a variety of tissues. In this article, we review two techniques that we have developed which take advantage of the unique characteristics of (31)P and (13)C MRS to investigate two distinct parameters of muscle mitochondrial metabolism; ATP production can be estimated by using the (31)P saturation-transfer technique, and oxidation via the TCA cycle can be modeled from (13)C MRS data obtained during the metabolism of a (13)C-labeled substrate. We will also examine applications of the techniques to investigate how these parameters of muscle mitochondrial metabolism are modulated in insulin resistant and endurance trained individuals.