The influence of three univalent salts (LiCl, and RbCl) on the separation of amino acids labelled with 3-(4-carboxybenzoyl)-quinoline-2-carboxaldehyde (CBQCA) in micellar capillary electrophoresis has been studied. Capacity factors for a series of eight CBQCA-labelled amino acids in a sodium dodecyl sulfate (SDS) micellar system containing different concentrations of salt were measured and were found to be related to both the hydrodynamic radius of the salt counter-ion (Li+, Na+, Rb+) and the relative hydrophobicity of the amino acid. Affinities of the analytes for the micelles were generally observed to decrease as the salt concentration in the background electrolyte was increased from 10 to 50 mM. This decrease in affinity was greatest in the presence of the salt counter-ion with the smallest hydrodynamic radius and is primarily due to an increased resistance to mass transfer. Furthermore, interaction of hydrophobic analytes with the micelles is greater than that of hydrophilic analytes at all salt concentrations due to the greater strength of the hydrophobic interactions and this effect is also enhanced in the presence of a smaller counter-ion. No negative effects due to Joule heating or electromigrative dispersion were observed for low to moderate concentrations of salt, which suggests that the use of simple univalent salts to modify analyte/micelle affinities can be a practical method for improving the separation of complex mixtures.