Phosphatidylcholine-passivated gold nanorods (NRs) adsorbed on polyanion-modified glass substrates. The NRs on glass substrates formed end-to-end assemblies showing red-shifted and broaden longitudinal surface plasmon (SP) bands. Addition of ammohexanethiol (AHT) induced dumping of SP bands but increased the density of NRs on glass surfaces. Thiol groups of AHT were effective to change the properties of NR assemblies on glass surfaces.