Magnetic nanoparticles exhibit unique nanoscale properties of superparamagnetism and have the potential to be utilized as excellent probes for magnetic resonance imaging (MRI). Especially, clinically benign iron oxide nanoparticles provide good MR probing capability and some of them are currently available for clinical applications. However, limited magnetic property and inability to escape from reticuloendothelial system (RES) of the currently used nanoparticles impede their further advancements and therefore it is necessary to develop advanced magnetic nanoparticle probes for next-generation molecular MR imaging. In this chapter, we overview recent progresses on the development of magnetic nanoparticle probes for molecular MR imaging. Utilization of these nanoparticle probes for both in vitro and in vivo molecular MR imaging will be described.