Chondrocytes have been widely used as tissue engineered seed cells for repair of focal cartilage lesions in clinic. However, in vivo behaviors of delivered chondrocytes are still poorly understood. In this study, the feasibility of in vivo tracking of superparamagnetic iron oxide nanoparticle (SPIO)-labeled chondrocytes by magnetic resonance imaging (MRI) for articular cartilage repair in minipig model was investigated. Results showed that chondrocytes were efficiently labeled by SPIO at optimal low dosages while maintaining essential cell properties. MRI SET2WI sequence revealed that marked hypointense signal void areas representing the transplanted labeled chondrocytes could be observed for at least 12 weeks. Histochemical staining confirmed the presence of Prussian blue-positive cells and GFP-positive cells at the hypointense signal void areas. These findings provide knowledge on the in vivo tracking of SPIO labeled chondrocytes on cartilage repair following transplantation in minipigs.