Magnetic resonance spectroscopy seeks to probe the normal biochemistry of organs and tissues in living subjects, which must be maintained as closely as possible to their normal physiology while immobilized in the bore of a magnet. This presents special challenges. This article describes the prescanning preparation required for small rodents, then typical inhalation anesthetic techniques and methods for monitoring the depth of anesthesia by means of respiration and heart rate. Techniques for immobilization of many anatomical locations, both internal and external, are described, together with consideration of the requirements for gating the scan sequence to minimize motion artefacts. The importance of maintaining normal temperatures is discussed, together with current methods for monitoring core temperature, the problems associated with supplying heat to maintain normal temperatures, and the advantages and disadvantages of the various options. Finally, requirements for the maintenance of animals, post-scanning, in order to optimize their condition for later scans in longitudinal studies are considered.