In this review, we summarize the latest developments and give a perspective on future applications of mesoporous silica nanoparticles (MSNs) in regenerative medicine. MSNs constitute a flexible platform for controlled delivery of drugs and imaging agents in tissue engineering and stem cell therapy. We highlight the recent advances in applying MSNs for controlled drug delivery and stem cell tracking. We touch upon novel functions of MSNs in real time imaging of drug release and biological function, and as tools to control the chemical and mechanical environment of stem cells. We discuss the need for novel model systems for studying biofunctionality and biocompatibility of MSNs, and how the interdisciplinary activities within the field will advance biotechnology research.