Mitochondrial function in muscle in vivo can be quantitatively evaluated using 31P magnetic resonance spectroscopy. In resting muscle the concentrations of ions (e.g., H+, Na+) and two of the major bioenergetic components (inorganic phosphate and creatine) are determined by regulated transcellular transport process. During recovery after exercise the kinetics and control of mitochondrial ATP synthesis can be established. During exercise the relative contributions to ATP of phosphocreatine conversion, anaerobic glycogenolysis and oxidative phosphorylation are dissected and have been shown to change with time. Thus the quantitative consequences of mitochondrial lesions and dysfunctions on these processes can be evaluated [1]. Studies of patients with mitochondrial disorders have been reported by many groups, including our own. For example, we used 31P-MRS to examine the skeletal muscle in 29 patients with mitochondrial myopathy [2]. Gastroncnemius was investigated in 15 patients and 30 normal subjects and finger flexor muscle in 24 patients and 35 normal controls. Results were abnormal in all but two patients. In 86% abnormalities were detected in resting muscle (mostly low phosphocreatine/ATP ratio, high [ADP] and low phosphorylation potential). Exercise and recovery increased the sensitivity of MRS in detecting abnormal metabolism. Nearly all patients (93%) showed abnormalities during recovery from exercise (slow phosphocreatine resynthesis, high [ADP] and its delayed recovery, providing increased drive for oxidative phosphorylation). Recovery of intracellular pH after exercise was significantly faster than normal, consistent with upregulation of proton efflux. Recently, the relationship between the nature of mitochondrial mutations and muscle bioenergetics is beginning to be examined, for example, in non-affected carriers of 11,778 mtDNA mutation [3] and in Leber’s hereditary optic neuropathy patients and carriers with the 14,484, 3460 and 11,778 mtDNA mutations [4]. Muscle mitochondrial abnormalities might also be present in other disorders such as familial hemiplegic migraine [5] and alternating hemiplegia of childhood [6]. MRS has also been used to study brain abnormalities in patients with mitochondrial disorders (e.g., MELAS) [4,5,7].