Quantum Dots (QDs), are considered as promising tools for biomedical applications. They have potential applications in agricultural industries, novel pesticide formulations, use in bio-labels and devices to aid genetic manipulation and post-harvest management. Since interactions with higher plants are of important environmental and ecological concern we investigated the cytotoxicity and genotoxicity of CdSe QDs in a model plant (Allium cepa) and established relationships between QDs genotoxic activity and oxidative stress. Allium cepa bulbs with intact roots were exposed to three concentrations of CdSe QDs (12.5, 25 and 50 nM). Cell viability and mitotic frequencies was measured for cytotoxicity, and to assess the genotoxicity DNA lesions, chromosome aberrations and micronuclei were evaluated. We report that QDs exerted significant genotoxic effects, associated with oxidative stress. This could be correlated with the retention of Cd in Allium roots as a dose-dependent increase with the highest uptake at 50 nM of CdSe QD. Oxidative stress induced by CdSe QD treatment activated both, antioxidant (SOD, CAT) scavengers and antioxidant (GPOD, GSH) enzymes. Concentrations as low as 25 nM CdSe QDs were cytotoxic and 50 nM CdSe QDs was found to be genotoxic to the plant. These findings enable to determine the concentrations to be used when practical applications using nanodevices of this type on plants are being considered.