Cadmium (Cd) contamination in agricultural soil and accumulation in rice poses serious threat to human health. It is reported that Selenium (Se) can mitigate the toxic effect of Cd in rice. But the underlying mechanism of Se preventing the Cd accumulation and restoring the micronutrient content in rice grains have not been studied before. Therefore, our main aim is to reduce Cd content and restore micronutrient content in rice grain and study the mechanism. Two indigenous rice genotypes (Maharaj and Jamini) were exposed to 10 and 50 mu M Cd in presence and absence of Se (5 mu M) with a control set and assessed for plant growth, biomass, Cd content, ROS and antioxidants for Cd induced toxicity and amelioration. Genes for micronutrient transporters were studied by RT-PCR. Grain Cd and micronutrient content and agronomic parameters were also studied. Se supplementation increased plant growth, biomass, and yield under Cd stress. SEM and EDX analysis revealed that Se-Cd complex formed on root surfaces restricted Cd uptake by the roots preventing root damage. Soil analysis confirmed that Se decreased Cd bioavailability, restricted root to shoot Cd translocation, ultimately reducing Cd accumulation and restoring micronutrients in grain. This was further validated by fluorescent Leadmium dye staining. In (Se + Cd) treated seedlings, up-regulation of S metabolism and nutrient transporter genes also contributed to the mitigation of Cd stress. The Se supplementation can be considered as a cost-effective, ecofriendly and sustainable approach to produce Cd free rice cultivation in Cd polluted soil.