High-performance capillary electrophoretic separation of bases, nucleosides, and nucleotides has been achieved with the use of sodium dodecyl sulfate, SDS, micelles. Rapid separations have been demonstrated with extremely narrow peak widths. Since the bases and nucleosides are uncharged at the pH of operation (pH 7), separation is a result of differential partition within the interior of the micelle; the more hydrophobic the species, the larger the partition coefficient and the larger the retention. Oligonucleotides are negatively charged and can be separated without SDS micelles; however, the time window is narrow and separation of complex mixtures limited. The combination of low concentrations of divalent metals and SDS micelles leads to a significant enhancement of the time window and good separation of oli-gonucleotides with high theoretical plate counts. The metal ion is electrostatically attracted to the surface of the micelle and differential metal complexation of the oligonucleotides with the surface of the micelle leads to separation of complex mixtures. As an example, 14 out of a mixture of 18 oligo-nucleotides of 8 bases, each with a different sequence, is achieved in less than 30 min by using a buffer system containing zinc and SDS micelles. © 1987, American Chemical Society. All rights reserved.