The work describes a simple and convenient process for highly efficient and direct DNA separation with functionalized silica-coated magnetic nanoparticles. Iron oxide magnetic nanoparticles and silica-coated magnetic nanoparticles were prepared uniformly, and the silica coating thickness could be easily controlled in a range from 10 to 50 nm by changing the concentration of silica precursor (TEOS) including controlled magnetic strength and particle size. A change in the surface modification on the nanoparticles was introduced by aminosilanization to enhance the selective DNA separation resulting from electrostatic interaction. The efficiency of the DNA separation was explored via the function of the amino-group numbers, particle size, the amount of the nanoparticles used, and the concentration of NaCl salt. The DNA adsorption yields were high in terms of the amount of triamino-functionalized nanoparticles used, and the average particle size was 25 nm. The adsorption efficiency of aminofunctionalized nanoparticles was the 4-5 times (80-100%) higher compared to silica-coated nanoparticles only (10-20%). DNA desorption efficiency showed an optimum level of over 0.7 M of the NaCl concentration. To elucidate the agglomeration of nanoparticles after electrostatic DNA binding, the Guinier plots were calculated from small-angle X-ray diffractions in a comparison of the results of energy diffraction TEM and confocal laser scanning microscopy. Additionally, the direct separation of human genomic DNA was achieved from human saliva and whole blood with high efficiency.