A novel method for direct separation of the enantiomers of salsolinol and N-methylsalsolinol was devised. The enantiomers were completely separated with ion-pair chromatography on a reversed-phase column with beta-cyclodextrin as a chiral mobile phase additive and sodium 1-heptanesulfonate as a counterion. The mechanism for enantioseparation with this ion-pair system containing beta-cyclodextrin was discussed. The effects of beta-cyclodextrin, counterions, pH, ionic strength, and organic solvent on retention were investigated, and a retention model was proposed and proved to be consistent with the experimental data. A preliminary study of the enantiomeric composition of salsolinol and N-methylsalsolinol in banana and in human brain was made as an example of the application of this assay.