Quantum dots play an important role in the in vitro, ex vivo, and in vivo optical imaging. Dramatic improvements have been achieved in the aspect of surface modification, biocompatibility, and targeting specificity, which had significant impact on the in vivo applications of quantum dots. This review summarizes the recent advances of quantum dots for in vivo imaging using both non-specific and targeted approaches. The toxicity of cadmium chalcogenide materials and alternative approaches such as the use of doped nanocrystal quantum dots were also discussed. The integration of quantum dots with other imaging techniques is also expected to give rise to a new generation of multifunctional probes for biomedical applications.