The potential for the metal nanocatalyst to contaminate vapour-liquid-solid grown semiconductor nanowires has been a long-standing concern, because the most common catalyst material, Au, is highly detrimental to the performance of minority carrier electronic devices. We have detected single Au atoms in Si nanowires grown using Au nanocatalyst particles in a vapour liquid-solid process. Using high-angle annular dark-field scanning transmission electron microscopy, Au atoms were observed in higher numbers than expected from a simple extrapolation of the bulk solubility to the low growth temperature. Direct measurements of the minority carrier diffusion length versus nanowire diameter, however, demonstrate that surface recombination controls minority carrier transport in as-grown n-type nanowires; the influence of Au is negligible. These results advance the quantitative correlation of atomic-scale structure with the properties of nanomaterials and can provide essential guidance to the development of nanowire-based device technologies.