Stem cell based therapies have critical impacts on treatments and cures of diseases such as neurodegenerative or cardiovascular disease. In vivo tracking of stem cells labeled with magnetic contrast agents is of particular interest and importance as it allows for monitoring of the cells' biodistribution, viability, and physiological responses. Here, recent advances in tracking and quantification of superparamagnetic iron oxide (SPIO) nanoparticle-labeled cells with magnetic resonance imaging, a noninvasive approach that can longitudinally monitor transplanted cells, are introduced. This is followed by recent translational research on human stem cells that are dual-labeled with green fluorescence protein and SPIO nanoparticles, then transplanted and tracked in a chicken embryo model. Cell labeling efficiency, viability, and cell differentiation are also presented.