The electrophoretic behaviour of a series of 33 different synthetic peptides has been investigated using free solution high-performance capillary zonal electrophoretic (HPCZE) methods. The dependency of the electrophoretic mobility, mu(em), on the peptide charge, q, and on the charge-to-size ratio parameter, zeta, determined according to several electromobility models, have been examined. Significant divergences from linearity in the mu(em) vs. q or the mu(em) vs. zeta plots were noted for several peptides, possibly due to the proclivity of specific arrangements of their amino acid sequences to assume preferred alpha-helical or beta-sheet conformational features rather than random coil structures under the HPCZE conditions. These results provide further demonstration of the facility of HPCZE procedures to probe the effects of compositional, sequential and conformational differences of closely-related peptides and their consequences on their physicochemical behaviour in solution.