Animal studies have shown some success in the use of stem cells of diverse origins to treat heart failure and ventricular dysfunction secondary to ischemic injury. The clinical use of these cells is, therefore, promising. In order to develop effective cell therapies, the location, distribution and long-term viability of these cells must be evaluated in a noninvasive manner. MRI of cells labeled with magnetically visible contrast agents after either direct injection or local or intravenous infusion has the potential to fulfill this goal. In this Review, techniques for labeling and imaging a variety of cells will be discussed. Particular attention will be given to the advantages and limitations of various contrast agents and passive and facilitated cell-labeling methods, as well as to imaging techniques that produce negative and positive contrast, and the effect on image quantification of compartmentalization of contrast agents within the cell.