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This paper describes recent progress of an investigation of the synthesis, processing, assembly and activation of gold nanoparticles that are of potential interest to fuel cell catalysis. Core-shell type gold nanoparticles of a few nanometer core size with organic monolayer encapsulation are highlighted. The activation of the core-shell nanoparticle assemblies towards nanostructured catalyst for potential fuel cell catalytic reactions is discussed. The understanding of the control factors in terms of nanocrystal size and interparticle spatial properties has important implications to the design of highly active nanogold catalysts for practical applications.