Suitably integrating multiple nanomaterials into nanostructured particle systems with specific combinations of properties has recently attracted significant attention in the research community. In particular, numerous particle systems have been designed and fabricated by integrating diverse materials with monodispersed silica nanoparticles. One or more distinct nanomaterials can be assembled on, encapsulated within, or integrated both inside and on the surface of silica nanoparticles using different chemistries and techniques to create multifunctional nanosystems. Research on these particle systems for biomedical applications has progressed rapidly during recent years due to the synergistic advantages of these complexes compared to the use of single components. This feature article surveys recent research progress on the fabrication strategies of these nanoparticle systems and their applications to medical diagnostics and therapy, thereby paving the way for the emerging field of nanomedicine.