Near-infrared spectroscopy (NIRS) is a non-invasive method for monitoring oxygen availability and utilization by the tissues. In intact skeletal muscle, NIRS allows semi-quantitative measurements of haemoglobin plus myoglobin oxygenation (tissue O2 stores) and the haemoglobin volume. Specialized algorithms allow assessment of the oxidation-reduction (redox) state of the copper moiety (CuA) of mitochondrial cytochrome c oxidase and, with the use of specific tracers, accurate assessment of regional blood flow. NIRS has demonstrated utility for monitoring changes in muscle oxygenation and blood flow during submaximal and maximal exercise and under pathophysiological conditions including cardiovascular disease and sepsis. During work, the extent to which skeletal muscles deoxygenate varies according to the type of muscle, type of exercise and blood flow response. In some instances, a strong concordance is demonstrated between the fall in O2 stores with incremental work and a decrease in CuA oxidation state. Under some pathological conditions, however, the changes in O2 stores and redox state may diverge substantially.