Nanoparticles are found very common in nature. For instance, proteins exist in almost all biological systems and metal-oxide nanoparticles are easily produced etc. Iron oxide nanoparticles with unique magnetic properties have a high potential to use in several biomedical, bioengineering and in vivo applications, including tissue repair, magnetic resonance imaging, immunoassay, drug delivery, detoxification of biologic fluids, cell sorting, and hyperthermia. Although various surface modifications are being done for making these nonbiodegradable nanoparticles more biocompatible . But their toxic potential is still a major concern. Therefore, it is necessary to use further examination assay systems in order to check nanoparticle effects. In this study, genotoxic potential of <50 nm and <100 nm Fe2O3 nanoparticles were investigated by using Comet Assay. Allium cepa root meristems were exposed with five doses (0.001, 0.01, 0.1, 1, 10 mM) of <50 nm for 4 hour and three doses (2.5, 5 (EC50), 10 mM) for <100 nm of Fe2O3 nanoparticle for 24 and 96 h. Methyl methanesulfonate -MMS (10 ppm) was used as a positive control. The results were also analyzed statistically by using SPSS by Windows, 18.0. It was determined that different doses of <50 nm Fe2O3 nanoparticle have no genotoxic effect of DNA. Different doses of <100 nm Fe2O3 have no genotoxic but only 10 mM dose have genotoxic effect on DNA. When compared <50 nm with <100 nm of Fe2O3 nanoparticle; <50 nm have more effects than <100 nm of Fe2O3 on DNA damage.