Fluorous chemistry, involving the use of a fluorous label for the functionalization of a substrate and a fluorous solvent for extraction of the functionalized substrate, is shown to be effective in solubilizing gold and CdSe nanoparticles in a fluorous medium, through phase transfer from an aqueous or a hydrocarbon medium. While these nanoparticles were functionalized with a fluorous thiol, single-walled carbon nanotubes and ZnO nanorods could be solubilized in a fluorous medium by reacting them with a fluorous amine. Fluorous chemistry enables the solubilization of the nanostructures in the most nonpolar liquid medium possible.