Stem cell-based therapy has the potential to improve the prospect of patients suffering from many untreatable diseases. Applications of stem cells for therapy of neurological conditions, such as Parkinson’s disease, Alzheimer’s disease, multiple sclerosis, or stroke, are particularly appealing as damage of the central nervous system is irreversible and the efficacy of conventional therapy is limited. Despite a broad interest among researchers and clinicians, progress in this field has been slow due to the remarkable complexity of the brain, which makes the task of repairing damaged tissue with stem cells extremely challenging. Making advances can be expedited by novel technologies that can monitor transplanted cells non-invasively. In vivo cellular imaging allows for the repetitive, real-time observation of targeted cells over the course of treatment without the need for invasive biopsies. Magnetic resonance imaging (MRI) is an excellent non-invasive cellular imaging modality as it has superior resolution, is widely used clinically, and has no radiation. This technique currently requires magnetic labeling of cells using superparamagnetic iron oxide particles (SPIOs) and transfection agents. In this chapter, methods for cellular labeling with SPIOs, transplantation of stem cells into the mouse brain, and MR imaging of the cells both in vivo and postmortem will be described. Additional histological and immunohistochemical procedures for analysis of the transplanted cells and the diseased brain environment are also provided.