The administration of exogenous stem cells offers promise to regenerate many damaged organs. However, failures of these cellular therapies could be related to many issues, such as the type of stem cell, the dose of cellular therapeutic, dosing regime, and mode of delivery. The recent ability to directly label stem cells with magnetic resonance (MR) contrast agents provides a simple, straight-forward manner to monitor accurate cell delivery and track stem cells non-invasively in a serial manner. Provided here is an overview of the currently available MR-labeling methods, including direct non-specific labeling with contrast agents, indirect specific labeling with contrast agents, labeling with MRI reporter genes, and fluorine hot spot labeling. Several of these approaches have now been applied successfully in preclinical animal models of cardiovascular disease. Once properly implemented, future clinical trials may benefit greatly from imaging stem cells with MRI.