Capillary electrophoresis (CE) methods for transferrin analysis are widely used in clinical laboratories, but complement C3 peaks often overlap with carbohydrate-deficient transferrin peaks. In this study, we discovered that the electrophoretic mobility of the complement C3 peak could be controlled by adding carboxymethylcellulose (CMC) and dextran sulfate (DS) to the background electrolyte solution, probably because of adsorption of the polyanions to the proteins. The improved capillary electrophoresis method was developed using spermine, CMC, and DS as the background electrolyte solution additives. The carbohydrate-deficient transferrin concentrations determined using this system were in good agreement with those determined by HPLC, with acceptable reproducibility. These results suggest that this method has the potential to be developed into a new clinical test.