Disclosed is an automatic nucleic acid purification apparatus which can prevent pollution due to aerosol generated from a biological sample containing high concentration target nucleic acid when the biological sample containing the high concentration target nucleic acid is mixed with other biological sample containing low concentration target nucleic acid or not containing the target nucleic acid. Further, disclosed is an automatic nucleic acid purification apparatus which can be applied to all kinds of nucleic acid purification equipments for purifying a plurality of biological samples using a magnet rode or a multi-pipette block moving in two or three axial directions, and which can minimize pollution due to the aerosol generated from the biological sample containing high concentration target nucleic acid and also can obtain accurate results.