New core-shell structured NaYF(4):Yb(3+),Tm(3+)@Fe(x)O(y) nanocrystals, with 20 nm Yb(3+),Tm(3+)-co-doped NaYF(4) nanocrystals as a core and 5 nm Fe(x)O(y) nanocrystals as a shell, have been synthesized and characterized by TEM and XRD analysis. These core-shell nanocrystals exhibit excellent near-infrared upconversion luminescence (UCL) emission at 800 nm under excitation by a continuous-wave 980 nm laser and superparamagnetic properties with a saturation magnetization (Ms) of ∼12 emu/g. Water-soluble nanocrystals were obtained by surface ligand exchange of oleic acid-coated precursor nanocrystals, and their internalization within living cells has been investigated by laser scanning UCL microscopy. Furthermore, the obtained core-shell nanocrystals have been applied in dual-modality T(2)-enhanced magnetic resonance (MR) and UCL imaging in vivo of the lymphatic system. Moreover, the toxicity of NaYF(4):Yb(3+),Tm(3+)@Fe(x)O(y) nanocrystals has also been evaluated by MTT assay, IC50 values, and histological analysis of lymphatic node sections.