Upconversion luminescent nanoparticles are becoming more widely used as imaging contrast agents, due to their high resolution and penetration depth, and avoidance of tissue auto-fluorescence and photodamage to cells. Here, we prepared upconversion fluorescent nanocrystals from rare-earth Yb3+ and Ho3+ co-doped fluorapatite (FA∶Yb3+/Ho3+) suitable for long-term tracking and monitoring cartilage development (chondrogenesis) in bone marrow mesenchymal stem cells (BMSCs) in vitro and in vivo.