This paper describes the selective phase separation of cobalt metal nanoclusters within a PS25300-b-PMMA(25900) block copolymer. This selective phase separation was achieved due to the different reactivities of the functional groups in the blocks toward the metal fragments. Transmission electron micrographs showed that the cobalt clusters aggregated primarily in the poly(methyl methacrylate) block, while no cobalt nanoclusters were observed in the polystyrene block, thus creating a patterned distribution that coincided with the morphology of the block copolymer. Fourier transform infrared studies demonstrated the development of a reactive adsorption process between cobalt nanoclusters and the poly(methyl methacrylate) block, as evidenced by the appearance of new absorption bands corresponding to the formation of Co(CO)(4)(-) and COO- and the shift of C-C-O and C-O combination bands.