Objective To evaluate the efficacy of MRI for assessment of re-distribution of bone marrow mesenchymal stem cells injected intramyocardially in main organs (heart, liver, spleen and kidney) under different heart status (beating or arresting) in a porcine model. Methods Bone marrow-derived mesenchymal stem cells were obtained from the male swine and labeled with iron oxide during culture. Acute myocardial infarction was created in female swine, one week later, the survivors were randomly divided into 4 groups. Cardiopulmonary bypass was set up to arrest the heart, and then labeled cells (1×108) were intramyocardially injected into the border of the infracted myocardium in group 1 (n=6). The same volume of cells was grafted into the beating heart in group 2 (n=6). In group 3 and 4, saline was injected into either the arresting or beating myocardium. Three days later, re-distribution of stem cells and cardiac function were assessed by T2*WI and cine MRI, respectively. All animals were sacrificed for histology and real-time quantitative polymerase chain reaction (RT-PCR) of sex-determining region on Y-chromosome (SRY) investigation.The ANOVA and t test was used for statistics. Results The left ventricular end-diastolic volume (LVEDV) before transplantation for group 1-4 were: (56.8±5.3),(54.8±6.8),(57.4±4.3)and(56.8±2.8) ml, and after transplantation for group 1-4 were: (65.2±5.2),(63.2±3.7),(60.2±4.7)and(62.2±4.4) ml. The left ventricular end-systolic volume (LVESV) before transplantation for group 1-4 were: (33.5±7.6),(32.3±5.3),(33.5±3.6)and(32.7±4.6) ml,and after transplantation for group 1-4 were: (37.3±5.6),(36.3±6.9),(34.3±5.4)and(36.3±8.1) ml. The left ventricular EF values (LVEF) before transplantation for group 1-4 were: (42.3±7.2)%,(41.7±6.8)%,(41.8±8.6)% and(42.7±7.7)%,and after transplantation for group 1-4 were: (44.5±8.7)%,(43.1±7.4)%,(42.8±5.6)% and(43.3±8.4)%. The myocardial infarction area (MI) before transplantation for group 1-4 were: (6.5±2.1),(6.4±1.9),(6.5±2.5)and(6.4±2.6) cm2,and after transplantation for group 1-4 were: (6.4±2.3),(6.2±2.6),(6.3±2.5)and(6.4±2.8) cm2 . There were no statistical differences before and after transplantation in these 4 groups[P values of before and after transplantation for LVEDV, LVESV, LVEF,MI were >0.05 (F= 0.277, 0.066,0.066, 0.003); and >0.05 (F= 1.137,0.182,0.021,0.008),respectively]. The T2 value of the infracted myocardium in group 1 decreased more obviously than that in group 2[(-22.3 ± 2.2) vs (-17.0 ± 0.8) ms, t=-5.489, P＜0.01], while the T2 value of the spleen decreased more significantly in group 2 than that in group 1[(-7.7 ± 0.7) vs (-13.3 ± 1.1) ms,t=9.055, P＜0.01]. The T2 values of the liver and kidney were no significant differences in group 1 and 2 (liver, t=-0.532,P>0.05 and kidney, t=-0.113,P>0.05). The results of RT-PCR in group 1 and 2 showed significant differences in heart[(150±62) vs (72±4) U/L ,P<0.05, t=3.109], spleen[(131±1) vs (233±17) U/L, P＜0.01, t=- 13.286]and liver[(17±1) vs (9±5) U/L ,P<0.01,t= 3.492]. Pathological examination demonstrated that the transplanted stem cells were positive for Prussian blue staining, which had a good correlation with MRI results. Conclusion MRI can serve as a convenient and efficient imaging method to track the migration of stem cells with SPIO labeled in early stage and evaluate its early re-distribution in vivo. Injection of bone marrow mesenchymal stem cells in the arresting heart could favor retaining more cells in the myocardium.