This paper describes a new method for self-assembling multifunctional nanocomposites with a magnetic core of iron oxide Fe(3)O(4) and a shell of CdSe/ZnS quantum dots (QDs). Two sol-gel processes were applied to form the uniform magnetic seeds (Fe(3)O(4)@SiO(2)-SH) and then the thiol coordination was used to bind the CdSe/ZnS QDs to the surface of the seeds. The multifunctional nanocomposites were characterized by means of transmission electron microscopy, X-ray diffraction, energy disperse spectroscopy, fluorescence spectroscopy, infrared spectroscopy, and superconducting quantum interference device (SQUID) magnetometer. The results showed that the magnetic Fe(3)O(4) nanoparticles and the CdSe/ZnS fluorescent QDs were combined together. The nanocomposites were of spherical shape with a mean diameter of 25 nm and exhibited well magnetic response, photostability, chemical activity, and water miscibility. The method put forward here can also be extended to combine systems of other metal oxides and QDs to fabricate core-shell nanocomposites with multifunction for biomedical applications.