Aqueous two-phase systems (ATPSs) formed by spontaneous phase separation of different water-soluble polymers are bio-compatible. Aqueous two-phase electrophoresis, coupling traditional solvent extraction with electrophoresis, is a novel separation technique and provides a successful method for separating mixtures of biomolecules. In this work, the selective recovery of amino acids by aqueous two-phase electrophoresis was examined with dextran-polyethylene glycol-water as a working system. The experiment results show that glutamic acid can be separated from phenylalanine and tryptophan successfully. The influences of the electrophoresis time, field strength, and phase volume ratio were studied in an intermittent separation equipment.