This paper describes the results of an investigation of the structure and composition of core-shell gold and alloy nanoparticles as catalytically active nanomaterials for potential fuel cell catalysis. Centered on the electrocatalytic methanol oxidation, we show three sets of results based on electrochemical, surface, and composition characterizations. First, electrochemical studies have revealed that the nanostructured catalysts are active towards the electrooxidation of methanol and carbon monoxide. Second, X-ray photoelectron spectroscopy (XPS) data have shown that the organic encapsulating shells can be effectively removed electrochemically or thermally, which involves the formation of oxides on the nanocrystals. Thirdly, direct current plasma - atomic emission spectrometry (DCP-AES) has revealed insights for the correlation of the composition of alloy nanoparticles with the catalytic activities. Implications of these results to the design of nanostructured catalysts will also be discussed.