Here, we report three-dimensional (3-D) visualization of dendrimer-encapsulated Pt nanoparticles (Pt DENs) by using 3-D electron tomography to reveal intricate structural characteristics of their whole organic-inorganic hybrid nanostructure. We reconstructed the 3-D spatial volume of Pt DENs by back-projecting a tilt series of two-dimensional (2-D) projections of Pt nanoparticles encapsulated inside dendrimers negatively stained with uranyl acetate. The direct 3-D visualization of Pt DENs elucidated their encapsulation characteristics with the spatial imaging of Pt nanoparticles embraced inside dendrimers in three dimensions. The encapsulation characteristics of Pt DENs were further verified with selective electrochemical poisoning experiments. In addition, quantitative 3-D structural characterization of Pt DENs provided more accurate and precise size distributions of nanoparticles than those obtained from conventional 2-D transmission electron microscopy analysis relying only on a 3-D structure projected on a 2-D plane.