Small polyhedral superparamagnetic iron oxide (SPIO) nanoparticles (<10 nm) coated with a thin layer of silica were prepared (SPIO@SiO(2) and SPIO@SiO(2)-NH(2)). Surface modification of the small polyhedral silica-coated SPIO nanoparticles with amines led to substantially higher mesenchymal stem cell (MSC) labelling efficiency without the use of additional transfecting agents. Therefore, amine surface-modified nanoparticles (SPIO@ SiO(2)-NH(2)) appeared to be the preferred candidate for MSC labelling. In vitro studies demonstrated that controlled labelling of SPIO@SiO(2) and SPIO@SiO(2)-NH(2) did not cause MSC death or proliferation inhibition. MSCs labelled with SPIO@SiO(2)-NH(2) nanoparticles retained differentiation potential and showed osteogenic, adipogenic and chondrogenic differentiations. The noncytotoxic polyhedral SPIO@SiO(2)-NH(2) nanoparticle-labelled MSCs were successfully implanted in rabbit brain and erector spinae muscle, and demonstrated long-lasting, durable MRI labelling efficacy after 8-12 weeks.