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Background Superparamagnetic iron oxide (SPIO) particles have shown much promise as a means to visualize labeled cells using molecular magnetic resonance imaging (MRI). Micrometer-sized superparamagnetic iron oxide (MPIO)particles and nanometer-sized ultrasmall superparamagnetic iron oxide (USPIO) are two kinds of SPIO widely used for monitoring stem cells migration. Here we compare the efficiency of two kinds of SPIO during the use of stem cells to treat acute myocardial infarction (AMI).Methods An AMI model in swine was created by 60 minutes of balloon occlusion of the left anterior descending coronary artery. Two kinds of SPIO particles were used to track after intracoronary delivered 107 magnetically labeled mesenchymal stem cells (MR-MSCs). The distribution and migration of the MR-MSCs were assessed with the use of 3.0T MR scanner and then the results were confirmed by histological examination.Results MR-MSCs appeared as a local hypointense signal on T2 -weighted MRI and there was a gradual loss of the signal intensity after intracoronary transplantation. All of the hypointense signals in the USPIO-labeled group were found on T2 -weighted MRI, contrast to noise ratio (CNR) decreased in the MPIO-labeled group (16.07±5.85 vs. 10.96±1.34)and USPIO-labeled group (11.72±1.27 vs. 10.03±0.96) from 4 to 8 weeks after transplantation. However, the hypointense signals were not detected in MPIO-labeled group in two animals. MRI and the results were verified by histological examination.Conclusions We demonstrated that two kinds of SPIO particles in vitro have similar labeling efficiency and viability.USPIO is more suitable for labeling stem cells when they are transplanted via a coronary route.