Manganese‐zinc ferrite nanoparticles were synthesized by using a hydrothermal treatment, coated with silica, and then tested as efficient cellular labels for cell tracking, using magnetic resonance imaging (MRI) in vivo. A toxicity study was performed on rat mesenchymal stem cells and C6 glioblastoma cells. Adverse effects on viability and cell proliferation were observed at the highest concentration (0.55 mM) only; cell viability was not compromised at lower concentrations. Nanoparticle internalization was confirmed by transmission electron microscopy. The particles were found in membranous vesicles inside the cytoplasm. Although the metal content (0.42 pg Fe/cell) was lower compared to commercially available iron oxide nanoparticles, labeled cells reached a comparable relaxation rate R2, owing to higher nanoparticle relaxivity. Cells from transgenic luciferase‐positive rats were used for in vivo experiments. Labeled cells were transplanted into the muscles of non‐bioluminescent rats and visualized by MRI. The cells produced a distinct hypointense signal in T2‐ or T2*‐weighted MR images in vivo. Cell viability in vivo was verified by bioluminescence. Track and trace: Nanoparticles with manganese‐zinc ferrite cores coated with silica are synthetized, characterized, and used as cell labels for cell tracking using magnetic resonance imaging (MRI). Particles enabled noninvasive visualization of transplanted labeled cells in vivo using MRI; their viability was verified by bioluminescence. [ABSTRACT FROM AUTHOR]