Selenium modified ruthenium nano-particles are of interest as methanol tolerant electro-catalysts replacing the rare and expensive platinum at the cathode side of low-temperature Direct Methanol Fuel Cells. Recently, it has been found that both the activity and the oxidation resistance of ruthenium can be improved significantly by selenium. The structure and chemical composition of that RuSe(x)O(y) electro-catalyst were analyzed by Anomalous Small Angle X-ray Scattering (ASAXS). ASAXS represents a powerful tool that yields not only averaged structural parameters, but also useful data on the chemical composition on the sub-nanometer scale. Comprehensive ASAXS measurements using X-ray energies near below the Se-K- and Ru-K- absorption edges have been performed in addition to XRD, EXAFS, XPS and TEM studies of these catalysts. The results obtained allowed to deduce a structural model. A cluster like distribution of sub-nanometer sized selenium on the surface of carbon black supported ruthenium nano-particles has been proven.