Ruthenium nanoparticles have been prepared by hydrogenation of the complex Ru(COD)(COT) (COD = 1,5-cyclooctadiene, COT = 1,3,5-cyclooctatriene) in the presence of i) heavily fluorinated solid compounds as stabilizers (para-bis(perfluorooctyl)benzene, 2,4,6-tris(perfluorooctyl)aniline, and the non-functionalized 11H,11H,12H,12H,13H,13H,14H,14H,15H,15H,16H, 16H-perfluorohexacosane (C10F21-(CH2)(6)-C10F21)); and ii) the liquid 1H,1H,2H,2H-perfluorodecylamine. The particles have been characterized by IR spectroscopy, elemental analysis, transmission electron microscopy (TEM), high-resolution TEM, wide- and small-angle X-ray scattering (WAXS and SAXS), and scanning electron microscopy with a field-emission gun (SEM-FEG). TEM images indicate the presence of aggregated small nanoparticles with a regular mean size of ca. 3 nm. These nanoparticles display the hexagonal close-packed structure of bulk ruthenium, as shown by WAXS analysis. HRTEM and SEM-FEG analyses reveal the tendency of the particles to self-assemble into superstructures (spheres) that can be more or less well defined depending on the fluorinated compound and/or the reaction conditions. This behavior has been confirmed in one case by SAXS measurements attesting the presence of small nanoparticles that are closely packed into clusters.