High-speed counter-current chromatography (HSCCC) is a continuous liquid-liquid partition chromatography, with remarkable advantages of high separation efficiency and no adsorption or denaturation by solid phase. The retention of stationary phase and the separation of proteins in polyethylene glycol 1000 (PEG1000)-phosphate aqueous two-phase system (ATPs) were studied with a multi-column high speed-counter-current chromatograph. The flow direction and speed of the mobile phase, and the rotation direction and speed of the apparatus showed different effects on the retention of the stationary phase, which reached the maximum at 33.3% with a flow rate of 0.6 mL/min and a rotation speed of 900 r/min in 14.0% PEG1000-16.0% phosphate ATPs. Distinct differences in partition coefficients among cytochrome C, lysozyme and hemoglobin were found at pH 9.2 and these three proteins were successfully separated in 14.0% PEG1000-16.0% phosphate ATPs at pH 9.2 by HSCCC with the apparatus rotating at 850 r/min and the mobile phase flow rate of 1.0 mL/min. The major protein components in hen egg white, including ovaltransferrin, ovalbumin and lysozyme also show distinct differences of partition coefficients in PEG1000-phosphate ATPs at pH 9.2. Ovalbumin and lysozyme were successfully purified to homogeneity and ovaltransferrin to ca 60% purity from the hen egg white sample with yields over 90% in 15.0% PEG1000-17.0% phosphate ATPs at pH 9.2 with the apparatus rotating at 850 r/min and mobile phase flow rate of 1.0 mL/min.