Magnetic resonance spectroscopy (MRS) and magnetic resonance imaging (MRI) are new and powerful tools to study tissue biochemistry, and to provide precise anatomical visualization of soft tissue structures. This review focuses on the use of these techniques to study exercise-induced muscle injury. MRS measurements show an increase in the ratio of inorganic phosphate to phosphocreatine (Pi/PCr) 1-7 d after eccentric exercise. This increase in Pi/PCr could be due to either increases in extracellular Pi or small increases in resting muscle metabolism. Increased Pi/PCr is also seen during training programs and may indicate persistent muscle injury. Increased resting Pi/PCr with injury was not associated with altered metabolism during exercise. Elevations in resting Pi/PCr have been used to show increased susceptibility of dystrophic muscle to exercise-induced injury. Progressive clinical deterioration in dystrophic dogs is marked by impaired muscle metabolism, and the presence of low oxidative muscle fibers not seen in normal dogs. MRI shows increased proton T2 relaxation times following eccentric exercise that last up to 80 d after injury, and can reflect muscle edema as well as longer lasting changes in the characteristics of cell water. MRI demonstrate precise localization of the injured area, with large differences in both location and degree of injury in different subjects following the same exercise protocol. Thus, MRS can provide information on the metabolic response to injury, while MRI provides information regarding the site and extent of the injury. These tools have promise in helping to understand exercise-induced muscle injury.