AuPd nanoparticles were prepared following a methodology designed to produce core-shell structures (Au core and Pd shell). Characterisation suggested slow addition of the shell metal favoured deposition onto the pre-formed core, whereas more rapid addition favoured the formation of a monometallic Pd phase in addition to some nanoparticles with core-shell morphology. When used for the selective hydrogenation of acetylene, samples which possessed monometallic Pd particles favoured over-hydrogenation to form ethane. A sample prepared by slow addition of a small amount of Pd resulted in the formation of a core-shell structure but with an incomplete Pd shell layer. This material exhibited completely different product selectivity with ethylene and oligomers forming as the major products as opposed to ethane. The improved performance was thought to be as a result of the absence of Pd particles which were capable of forming a Pd-hydride phase with enhanced oligomer selectivity associated with reaction on uncovered Au atoms.