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In this article, we present new samples of lamellar magnetic nanocomposites based on the self-assembly of a polystyrene-b-poly(n-butyl methacrylate) diblock copolymer synthesized by atom transfer radical polymerization. The polymer films were loaded with magnetic iron oxide nanoparticles covered with polystyrene chains grown by surface initiated-ATRP. The nanostructuration of the pure and magnetically loaded copolymer films on silicon was studied by atomic force microscopy, ellipsometry, neutron reflectivity and contact angle measurement. The present study highlights the strong influence of the copolymer extremity - driven itself by the choice of the ATRP chemical route - on the order of the repetition sequences of the blocks in the multi-lamellar films. In addition, a narrower distribution of the nanoparticles' sizes was examined as a control parameter of the SI-ATRP reaction.