A double junction interface was utilized to preserve separation efficiency and alleviate ion suppression from sulfated beta-cyclodextrin (S-beta-CD) in electrokinetic chromatography-electrospray ionization-mass spectrometry. The utility of the approach was demonstrated by chiral EKC-MS analysis of dihydroxyphenylalanine and methyldihydroxyphenylalanine enantiomers using either low concentration (counter-migration mode; 0.1% S-beta-CD) or high concentration (carrier mode; 2% S-beta-CD). In the counter-migration mode, S-beta-CD anions were supplied continuously from the junction reservoir to the separation column so that the effective separation length was preserved. This interface is especially useful under carrier mode in which high concentration of S-beta-CD will migrate toward the ESI source. With the use of the double junction interface, the S-beta-CD exited the separation column will remain in the junction reservoir, whereas the analyte will flow toward the ESI source through a connecting column. As a result, no ion suppression was observed and the sensitivity was improved significantly.