As recent reports suggest that nanoparticles may penetrate into cell membrane and effect DNA condition, it is necessary to assay possible cytotoxic and genotoxic risk. Three different sizes of magnetic nanoparticle silica (MNP@$SiO_2$) (50, 100 and 200 nm diameter) were tested for cytotoxicity and DNA damage using L5178Y cell. MNP@$SiO_2$ had constant physicochemical characteristics confirmed by transmission electron microscope, electron spin resonance spectrometer and inductively coupled plasma-atomic emission spectrometer for 48 h. Treatment of MNP@$SiO_2$ induced dose and time dependent cytotoxicity. At 6 h, 50, 100 or 200 nm MNP@$SiO_2$ decreased significantly cell viability over the concentration of 125 ${mu}g/ml$ compared to vehicle control (p<0.05 or p<0.01). Moreover, at 24 h, 50 or 100 nm MNP@$SiO_2$ decreased significantly cell viability over the concentration of 125 ${mu}g/ml$(p<0.01). And treatment of 200 nm MNP@$SiO_2$ decreased significantly cell viability at the concentration of 62.5 ${mu}g/ml$ (p<0.05) and of 125, 250, 500 ${mu}g/ml$ (p<0.01, respectively). Furthermore, at 48 h, 50, 100 or 200 nm MNP@$SiO_2$ decreased significantly cell viability at the concentration of 62.5 ${mu}g/ml$ (p<0.05) and of 125, 250, 500 ${mu}g/ml$ (p<0.01, respectively). Cellular location detected by confocal microscope represented they were existed in cytoplasm, mainly around cell membrane at 2 h after treatment of MNP@$SiO_2$. Treatment of 50 nm MNP@$SiO_2$ significantly increased DNA damage at middle and high dose (p<0.01), and treatment of 100 nm or 200 nm significantly increased DNA damage in all dose compared to control (p<0.01). Taken together, treatment of MNP@$SiO_2$ induced cytotoxicity and enhanced DNA damage in L5178Y cell.