Connections between the calculated and measured electrophoretic mobilities (mu(ep)) determined by capillary electrophoresis as well as connections between the measured and calculated diffusion coefficients of anti-tumor peptides have been investigated in background electrolytes (BGEs) containing different organic solvents (acetonitrile, methanol, ethanol and isopropanol). Comparison of the electrophoretic mobility (mu(ep)) values revealed discrepancies between the measured and calculated values. However, no change in the migration order or selectivity could be expected from the calculated mu(ep) values, variation of both properties was observed applying organic solvents as BGE modifiers. Experimental determination of the diffusion coefficient suggested that the effect of the organic solvents is not restricted to the change of the BGE viscosity. The reason for the discrepancy between the measured and calculated mobility values might be the possible conformation and/or solvation changes of the peptide caused by the different organic solvents.