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This paper demonstrates a novel facile method for fabrication of patterned arrays of gold nanoparticles on Si/SiO2 by combining electron beam lithography and self-assembly techniques. Our strategy is to use direct-write electron beam patterning to convert nitro functionality in self-assembled monolayers of 3-(4-nitrophenoxy)-propyltrimethoxysilane to amino functionality, forming chemically well-defined surface architectures on the 100 nm scale. These nanopatterns are employed to guide the assembly of citrate-passivated gold nanoparticles according to their different affinities for amino and nitro groups. This kind of nanoparticle assembly offers an attractive new option for nanoparticle patterning a silicon surface, as relevant, for example, to biosensors, electronics, and optical devices.