Aim: To study the specificity of cellular MRI based on superparamagnetic iron oxide particles (SPIOs), especially within the CNS. Materials & methods: A microglial cell line was engineered for the expression of a suicide gene, the receptor of diphtheria toxin (DT), and two reporter genes, green fluorescent protein and luciferase, in order to induce, in a controlled manner, cell death and test it through bioluminescence. SPIO-labeled DT-sensitive and control DT-insensitive cells were transplanted into the brains of mice, which underwent serial MRI and bioluminescence studies before and up to 90 days after DT-induced cell death. Results: No variations in SPIO signal voids were detected along longitudinal monitoring in brain hemispheres transplanted with DT-sensitive cells. Ex vivo analyses showed persistence of iron nanoparticle deposits at transplantation sites. Conclusion: Due to the long-term persistence of signal after transplanted cell death, caution is advised when SPIOs are employed for cell tracking. Original submitted 27 January 2014; Revised submitted 18 April 2014.