Ruthenium exhibits a high catalytic activity that is further enhanced when the material is used as nanosized particles. The origin of the enhanced performance lies in the highly increased surface to volume ratio and, often, to the surface/environment-driven structural relaxation taking place at the nanoscale. In this paper, we show how high-energy X-ray diffraction, atomic pair distribution function analysis, and reverse Monte Carlo simulations may be used to determine the 3-D structure of nanoparticle catalysts such as Ru with sizes less than 5 nm. Ruthenium particles that are 4 nm in size are found to possess a hexagonal close packed-type structure, similar to that found in bulk Ru. Particles that are only 2 nm in size are heavily disordered and consist of a Ru core and a Ru-S skin due to the usage of thiol-based capping agents. This work is the first application of an approach for determining the atomic-scale structure of nanosized catalysts based entirely on experimental diffraction data. The new structural information is a starting point for a better understanding of the structure-property relationship and, hence, for the design of improved nanosized catalysts, including Ru.