Gene and cell therapies convey high hopes for treatment of skeletal and heart muscle diseases. In the experimental protocols under development as well as in the first clinical trials, longitudinal control by an atraumatic procedure is needed. Nuclear magnetic resonance (NMR), via its two modalities, imaging or spectroscopy, should play a major role both for in vivo animal and human studies, because of the great number of parameters that can be measured, sequentially or simultaneously, and because of its aptitude to monitor several steps of protocols, in particular to detect physiological modifications induced by therapies. We review here the many possible applications of nuclear magnetic resonance in gene/cell therapies where muscle is the target organ, with emphasis on the application of nuclear magnetic resonance to functional studies.