The inner surface of fused silica capillaries has been covalently modified with different porphyrins (deuteroporphyrin, complexes of deuteroporphyrin with metal ions Fe(III), Cu(II), Zn(II), Ni(II), and Cu(II)-meso-tetra (carboxyphenyl) porphyrin) and it was applied for the separation of biologically active peptides by open-tubular capillary electrochromatography. Separations were performed in a mobile phase composed of 25 mM potassium phosphate, pH 4.0, 5% v/v ACN and 10 mM hydroquinone. Changes in the effective electrophoretic mobility of peptides were studied concerning porphyrin central metal atom, attachment geometry, and the presence of coordinating or aromatic amino acid residues in the peptide sequence. The results showed that differences in metal core on the porphyrin and the spatial conformation of attached porphyrin result in changes in the analyte interaction with the stationary phase.