Hydrophobic gold nanorods were fabricated from hydrophilic gold nanorods coated with hexadecyltrimethylammonium bromide by treating with mercaptopropyltrimethoxysilane (MPS) and subsequently octadecyltrimethoxysilane (ODS). The fabrication of the hydrophobic shell went through the process of (1) binding MPS onto the nanorods, (2) hydrolysis of methoxysilanes, and (3) immobilization of ODS by dehydration condensation. The 2- or 3-D ordered structures of hydrophobic nanorods were self-assembled by the evaporation of solvent on a substrate. The aspects of 2-D assemblies were dependent on the concentration of the nanorods, as was seen in transmission electron microscopic images. At a low concentration, the nanorods assembled parallel to the substrate, whereas they stood on the substrate at a high concentration. On the other hand, in a solid of the gold nanorods, the formation of the 3-D assembly was confirmed by small-angle X-ray scattering. The assembly consisted of hexagonal arrays of the gold nanorods and their lamellar accumulation.