The adult rodent brain contains neural progenitor cells (NPCs), generated in the subventricular zone (SVZ), which migrate along the rostral migratory stream (RMS) towards the olfactory bulb (OB) where they differentiate into neurons. The aim of this study was to visualize endogenous NPC migration along the RMS with magnetic resonance imaging (MRI) in adult healthy mice. We evaluated various in situ (in vivo) labeling approaches using micron-sized iron oxide particles (MPIOs) on their efficiency to label endogenous NPCs. In situ labeling and visualization of migrating NPCs were analyzed by a longitudinal MRI study and validated with histology. Here, we visualized endogenous NPC migration in the mouse brain by in vivo MRI and demonstrated accumulation of MPIO-labeled NPCs in the OB over time with ex vivo MRI. Furthermore, we investigated the influence of in situ injection of MPIOs on adult neurogenesis. Quantitative analysis of bromodeoxyuridine labeled cells revealed altered proliferation in the SVZ and NPC migration after in situ MPIO injection. From the labeling strategies presented in this report, intraventricular injection of a small number of MPIOs combined with the transfection agent poly-l-lysine hydrobromide was the best method as labeling of the NPCs was successful and proliferation in the SVZ was only marginally affected. While MRI visualization of endogenous NPC migration can provide insight into aberrant NPC migration in disease models, this work emphasizes the importance to carefully explore the impact on adult neurogenesis when new in situ labeling strategies are developed.