A novel preparative size-exclusion electrochromatography with an oscillatory low-voltage electric field perpendicular to the liquid phase streamline (pSEEC) was proposed with a column design of rectangular cross-section. The column of 12 cm length was packed with Sephadex G-75, and the retention behavior of bovine serum albumin (BSA) and myoglobin (Myo) was extensively investigated under various conditions. The results indicated that the partition coefficient of a charged protein increased significantly on increasing the current strength as well as the difference between its p/ and pH. The partition coefficient also increased on decreasing the mobile phase conductivity. For the gel-excluded protein like BSA, the concentration polarization (CP) on the gel surface induced by the protein electromigration was the main reason for the increased retention. For a gel-permeable protein like Myo, both the CP and electrophoretic migration in the solid phase contributed to its increased retention. Further results exhibited that the polarization would be offset by diffusion, because the accumulated protein would flux back to the bulk liquid phase. Therefore, when the electrically induced mass flux was equal to the diffusion flux, the partition coefficient did not change with a further increase of the oscillatory current cycle. Finally, pSEEC was compared with SEC in the separation of protein mixtures of BSA/Myo as well as BSA/ Myo/lysozyme. The results showed much better resolutions of the protein mixtures in pSEEC with the column as short as 12 cm. The potential of pSEEC for preparative protein separation was therefore demonstrated.