An apparatus and method for purification of nucleic acids of cells or viruses are provided. The nucleic acid purification apparatus includes: a cell lysis capillary having a sample inlet through which samples and magnetic beads are introduced; a vibrator attached to the capillary and mixing the samples and the magnetic beads in the capillary; a laser generator attached to the capillary and supplying a laser to the capillary; and a magnetic force generator attached to the capillary and fixing the magnetic beads to a capillary wall. According to the method and apparatus, PCR yield can be increased since PCR inhibitors can be readily removed by means of a phase separation in a capillary. The use of an electromagnet ensures the removal of the PCR inhibitors. In addition, since cell lysis and DNA purification process can be simultaneously performed, LOC steps can be reduced.