AuPd nanoparticles were prepared following a methodology designed to produce core-shell structures (an Au core and a Pd shell). Characterisation suggested that 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 the core-shell morphology. When used for the selective hydrogenation of acetylene, samples that possessed monometallic Pd particles favoured over-hydrogenation to form ethane. A sample prepared by the 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 a 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 are capable of forming a Pd-hydride phase, with enhanced oligomer selectivity associated with reaction on uncovered Au atoms.