Gold nanorods (GNRs) are strongly absorbing at near-infrared (NIR) frequencies and can be employed as multifunctional agents for biological imaging and theragnostics. GNRs can support nonlinear optical microscopies based on two-photon-excited luminescence and can enhance the contrast of biomedical imaging modalities such as optical coherence tomography and photoacoustic tomography. GNRs are also efficient at mediating the conversion of NIR light energy into heat and can generate localized photothermal effects. However, future clinical applications will require the rigorous removal of CTAB, a micellar surfactant used in GNR synthesis, and reliable methods of surface functionalization for cell-selective targeting and for minimizing nonspecific uptake into cells. This can be accomplished by using polystyrenesulfonate (PSS) as a sorbent for removing CTAB, and in situ dithiocarbamate formation for introducing chemisorptive ligands onto GNR surfaces.