Two sets of peptides, each having structurally similar amino acid sequences, have been investigated by capillary electrochromatography (CEC) using etched chemically modified capillaries as the separation medium. In comparison to gradient RP-HPLC, the resolving power of the described CEC methods has been found to be superior. A number of variables have been examined with respect to optimization of the separation of these closely related peptides with several different etched chemically modified capillaries. These experimental variables included the nature of the bonded moiety, the pH, the organic modifier type, and the amount of organic modifier in the buffer electrolyte. Systematic variation of these parameters results in significant changes in the migrational behavior of the investigated peptides and provides important insight into the underlying molecular separation processes that prevail in open tubular CEC. Moreover, under optimized conditions, efficient separations characterized by highly symmetrical peaks were achieved. In addition, this study has permitted the long-term stability as well as the short-term and long-term reproducibility of the etched chemically modified capillaries to be documented.