Small gold clusters (<1 nm), protected by monolayers of glutathione, N-(2-mercaptopropionyl)glycine, or mercaptosuccinic acid, were prepared by reducing the corresponding Au(I)-thiolate polymers and were fractionated by size using polyacrylamide gel electrophoresis (PAGE). Mass analysis of the fractionated clusters revealed that their core sizes varied with the molecular structures of the thiolates. This finding indicates that the reduction of the Au(I)-thiolate polymers yields small clusters whose growth is kinetically hindered by passivation with thiolates. Optical spectra of the clusters with identical compositions exhibited different profiles depending on the thiolate molecular structures. This observation implies that deformation of the underlying gold cores is induced by interligand interactions.