A novel method based on controlled etching was developed to fabricate nanopores on preformed silica nanoparticles (< 100 nm in diameter). The obtained monodisperse nanoporous particles could form highly stable homogeneous colloidal solution. Fluorescent silica nanoparticles and magnetic silica-coated gamma-Fe2O3 nanoparticles were investigated as examples to illustrate that this strategy could be generally applied to various silica-based functional nanoparticles. The results indicated that this method was effective for generating pores on these nanoparticles without altering their original functionalities. The obtained multifunctional nanoparticles would be useful for many biological and biomedical applications. These porous nanoparticles could also serve as building blocks to fabricate three-dimensionally periodic structures that have the potential to be used as photonic crystals.