Customizable ligand exchange of gold nanorods (NRs) is described. NRs are synthesized with the cationic surfactant cetyltrimethylammonium bromide (CTAB) which is exchanged with thiolated ligands that enable suspension in buffer. Exchange is achieved by a two phase extraction. First, CTAB is removed from the NR-CTAB by extracting the NRs into an organic phase via the ligand dodecanethiol (DDT). The NR-DDT are then extracted into an aqueous phase by mercaptocarboxylic acids (MCA), HS-(CH2)(n)-COOH (n = 5, 10, and 15). Ligands can be further customized to thiolated poly(ethylene glycol), PEG(MW) (MW = 356, 5000, and 1000). Ligand-exchanged NRs (NR-MCA and NR-PEG(MW)) are stable in buffer, do not aggregate, and do not change size upon ligand exchange. They can be run in agarose gel electrophoresis with narrow bands, indicating uniform charge distribution and enabling quantitative analysis. DNA functionalization of NR-MCA is straightforward and quantifiable, with minimal nonspecific adsorption.