Although conventional high-resolution transmission electron microscopy is a powerful method for the elucidation of the structure of mesoporous solids (diameter of pores from 1.5 to 20 nm), it is far less capable than high-resolution scanning transmission electron microscopy in identifying the spatial distribution of nanocrystals of catalysts encapsulated within the mesopores. Using high-angle annular dark-field imaging (either in a 100 or 300 keV STEM system), it is possible to locate precisely individual bimetallic nanoparticles (Ag3Ru10, Cu4Ru12 and Pd6Ru6 hydrogenation catalysts) supported on mesoporous silica, to determine their size distribution, and to record their characteristic X-ray emission maps. It is also established that there is little tendency for elemental fragmentation of the bimetallic catalysts, all of which were prepared by decarbonylating, by thermolysis, precursor cluster carbonylate anions: [Ag3Ru10C2(CO)(28)Cl](-), [Ru6C(CO)(16)Cu2Cl](2-) and [Ru6Pd6(CO)(24)](2-).