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Rat glioma cells were labeled using electroporation with either manganese oxide (MnO) or superparamagnetic iron oxide (SPIO) nanoparticles. The viability and proliferation of SPIO-labeled cells (1.9 mg Fe/ml) or cells electroporated with a low dose of MnO (100 μg Mn/ml) was not significantly different from unlabeled cells; a higher MnO dose (785 μg Mn/ml) was found to be toxic. The cellular ion content was 0.1–0.3 pg Mn/cell and 4.4 pg Fe/cell, respectively, with cellular relaxivities of 2.5–4.8 s−1 (R1) and 45–84 s−1 (R2) for MnO-labeled cells. Labeled cells (SPIO and low-dose MnO) were each transplanted in contralateral brain hemispheres of rats and imaged in vivo at 9.4T. While SPIO-labeled cells produced a strong “negative contrast” due to the increase inR2, MnO-labeled cells produced “positive contrast” with an increasedR1. Simultaneous imaging of both transplants with opposite contrast offers a method for MR “double labeling” of different cell populations. Magn Reson Med 60:1–7, 2008. © 2008 Wiley-Liss, Inc.