The strong absorption of gold nanoparticles in the visible spectral range allows the localized generation of heat in a volume of only a few tens of nanometer. The efficient conversion of strongly absorbed light by plasmonic gold nanoparticles to heat energy and their easy bioconjugation suggest that the gold nanoparticles can be used as selective photothermal agents in molecular cell targeting. The selective destruction of alkaline phosphatase, the permeabilization of the cell membrane and the selective killing of cells by laser irradiating gold nanoparticles were demonstrated. The potential of using this selective technique in molecularly targeted photothermal therapy and transfection is discussed.