A method for the templated DNA-directed self-assembly of individual gold nanoparticles (AuNPs) into discrete nanostructures is described. The templating nanostructures consisted of a linear configuration of six metal dots with a center-to-center dot distance of 55 nm, fabricated by means of electron beam lithography. The 40 nm DNA-capped AuNPs were immobilized onto this templating nanostructure to produce a linear configuration of six adjacent AuNPs. The geometry of the templating nanostructure was found to be critically important for the successful direction of a single nanoparticle onto individual adsorption sites. For optimized template structures the immobilization efficiency of nanoparticles onto the individual adsorption sites was found to be 80%. The nonspecific association of nanoparticles with specifically adsorbed nanoparticles and the between adsorption of nanoparticles, bridging two individual adsorption sites, were the two main defects observed in the immobilized assemblies. Less than 1% of all surface confined AuNPs adsorbed nonspecifically in the areas between the self-assembled regular arrays.