Hybrid sub-micrometer particles are of great interest and have been extensively applied to tailor the catalytic, electrical, optical, magnetic, mechanical or thermal properties of the material. Especially their application in the field of diagnostics and drug delivery systems is a rapidly advancing research area. They can serve as carriers for biomolecules like peptides or proteins and be applied for drug targeting, controlled drug release, immunoassays and immunodiagnostics. In the recent years, it has been shown that the miniemulsion is a very suitable technique to obtain hybrid polymeric particles in the size range tuneable from 50-500 nm. In this chapter, we are presenting several experimental procedures for the formulation of well-defined carboxyl- and amine-functionalized nanoparticles from the monomers (via radical polymerization) or preformed polymers (via solvent evaporation technique). Introduction of the fluorescent dye or/and magnetite into the reaction mixture leads to the formation of fluorescent nanoparticles with magnetic properties. The obtained particles were characterized in terms of their size, size distribution and amount of surface functional groups. Furthermore, the binding of targeting molecules to the carboxyl and amine groups is reported.