Palladium clusters protected by a series of n-alkanethiolates, Pd:SCn (SCn = n-CnH2n+1S, n = 10, 12, 14, 16, and 18), were prepared by a ligand exchange approach: Pd clusters protected by poly (N-vinyl-2-pyrrolidone) (PVP) were transferred from the aqueous phase to the toluene phase containing the thiols. The structures and stabilities of the thiolate monolayers of the Pd:SCn clusters were investigated by gel permeation chromatography (GPC) together with TEM, XPS, and FT-IR. The thicknesses of the thiolate layers formed on the Pd clusters were evaluated from the differences between the hydrodynamic diameters and core diameters of the Pd:SCn clusters, determined by GPC and TEM, respectively. The thicknesses thus obtained are in good agreement with the lengths of the corresponding thiolates in the all-trans conformations, illustrating that the alkanethiolates in nearly straight configurations are aligned almost perpendicularly to the core surfaces. Fractionation of the Pd:SC18 clusters by GPC yielded a series of the purified samples: the clusters in each fraction are different in their core sizes. The GPC measurements on the Pd:SCn clusters with small n revealed the decomposition of the monolayers through spontaneous etching and their reconstruction by heat treatment in the presence of the free thiols. The mechanism of these processes is discussed. The present study demonstrates that the GPC provides an elemental and versatile means to characterize and purify the monolayer-protected clusters.