In this study, we present a surface-modulated and highly biocompatible magnetic iron oxide (Fe3O4) nanocrystal probe that can be used for efficient intracellular labeling and their MRI applications. Specifically, we describe the preparation of these probes and the results from studies exploring their (1) transport into various cell types and MR contrast effect, (2) cytotoxicity, and (3) application in in vivo monitoring of neural stem cell migration in rat spinal cord.