We successfully developed a method to control the introduction of Pd nanoparticles selectively into the poly(2-vinylpyridine) (P2VP) microdomains of polyisoprene-block-poly (2-vinylpyridine) (PI-b-P2VP) diblock copolymer. The technique consists of three steps: (i) cross-linking of P2VP microdomains with diiodobutane (DIB), (ii) immersion of the cross-linked film in the mixture of palladium diacetate (Pd(acac)2), benzyl alcoho, and toluene, and (iii) annealing the immersed and dried film at 230 degrees C for 30 min. With this method, we could generate Pd nanoparticles with considerably uniform size (5.5 nm) by in situ reduction of the Pd ions solely within the P2VP microdomains without disturbing the regular microdomain structure of Pl-b-P2VP diblock copolymer. We employed 3D electron tomography to analyze the location and the size of the Pd nanoparticles and demonstrated its capability in the analysis of nanoparticle/block copolymer systems.