The CE separation of alpha-helical polypeptides composed of 14-31 amino acid residues has been investigated using aqueous and nonaqueous BGEs. The running buffers were optimized with respect to pH. Generally, higher separation selectivities were observed in nonaqueous electrolytes. This may be explained by a change in the secondary structure when changing from water to organic solvents. Circular dichroism spectra revealed a significant increase in helical structures in methanol-based buffers compared to aqueous buffers. This change in secondary structure of the polypeptides contributed primarily to the different separation selectivity observed in aqueous CE and NACE. For small oligopeptides of two to five amino acid residues no significant effect of the solvent was observed in some cases while in other cases a reversal of the migration order occurred when changing from aqueous to nonaqueous buffers. As these peptides cannot adopt secondary structures the effect may be attributed to a shift of the pK(a) values in organic solvents compared to water.