Very few chemical strategies for the selective functionalization of nanostructures have been developed despite their potential for controlling high-order assembly processes. We report a novel approach for the selective chemical functionalization and localized assembly of one-dimensional nanostructures (rods), based upon the systematic activation (DNA functionalization) and passivation (self-assembled monolayers) of specific surface sites through the use of orthogonal chemical reactions on electrochemically grown metal nanorod arrays in porous anodic aluminum oxide templates. The ability to orthogonally functionalize the ends or the side of a nanorod, as well as the gaps between two rods, with different DNA strands allows one to synthesize nanostructure assemblies that would be difficult to realize any other way and that could ultimately be utilized for making a wide variety of device architectures.