Saponinum album (SA) is a commercial mixture of saponins isolated from Gypsophila species. In the previously published work, we reported that SA dramatically improves the inhibition of tumor growth by targeted toxins in mice in a synergistic way. Here we report a simplified electrophoretic method for the isolation of a highly effective fraction of SA with a relative electrophoretic mobility to the dye front (R-f) of 0.63 from the mixture. In total, four different fractions were separated at a preparative scale, and evaluated by ESI-MS, HPLC and TLC analysis. Electrophoretic mobility and electrochemical properties of the different fractions of saponins from SA were set into relation to their ability to enhance the cytotoxicity of epidermal growth factor (EGF)-based targeted toxins. We here treated HER-14 cells, which are NIH-3T3 Swiss mouse embryo cells transfected with the human EGF receptor. Untransfected NIH-3T3 cells served as control. The major bulk of SA (72.3%) (R-f = 0.78) migrated the farthest and was found to be significantly ineffective (p<0.05) in enhancing the cytotoxicity of the targeted toxin, while the second fraction (R-f = 0.63) showed an enhancement of 9800-fold. The third (R-f = 0.56) had an enhancement factor of 3200, the fourth (R-f = 0.08) was again significantly ineffective (p<0.05) in exhibiting any enhancement of cytotoxicity.