Noninvasive monitoring of stem cells is an important step in developing stem-cell-based therapies. Among several imaging techniques available, magnetic resonance imaging (MRI) provides an effective way to detect implanted stem cells in live animals. In this mini-review, we discuss the available MRI contrast agents and different cell-labeling strategies used for detection of stem cell migration in the brain. The potential effects of MRI contrast agents on stem cell viability and differentiation are also discussed.