Three cysteine-based coated selectors, S-benzyl-(R)-cysteine, S-diphenylmethyl-(R)-cysteine and S-trityl-(R)-cysteine, have been used in the ligand-exchange separation of a selected set of natural and unnatural underivatized amino acids. With only few exceptions, a gain in enantiodiscrimination was obtained when the most lipophilic discriminating agent, characterized by the presence of a trityl moiety, was engaged. Moreover, a new descriptive structure-separation relationship study through molecular surface (Jurs) and shape (Shadow) descriptors provided evidence that specific physico-chemical features of the employed chiral selector result decisive in establishing which property of the analyte is responsible for the enantiorecognition accomplishment.