Nanoparticle-based drug delivery systems have considerable potential for improvement of drug stability, bioavailability, and reduced dosing frequency. Important technological advantages of nanoparticles include high carrier capacity across biological membranes and controlled drug release. Ultimately, success of nanodelivery systems depends on toxicologic issues associated with the understanding of the fate of nanocarriers and their polymeric constituents within the targeted cells. Here we describe a method for determining subcellular distribution of nanoparticles by isolation and identification of organelles that come in direct contact with these structures.