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This work investigated the thermoelectric properties of thin silicon membranes that have been decorated with high density of nanoscopic holes. These “holey silicon” (HS) structures were fabricated by either nanosphere or block-copolymer lithography, both of which are scalable for practical device application. By reducing the pitch of the hexagonal holey pattern down to 55 nm with 35% porosity, the thermal conductivity of HS is consistently reduced by 2 orders of magnitude and approaches the amorphous limit. With a ZT value of ∼0.4 at room temperature, the thermoelectric performance of HS is comparable with the best value recorded in silicon nanowire system.