Rice (Oryza sativa L.) seedlings differing in boron tolerance were grown in hydroponics containing varying boron concentration. (as boric acid) for 8 days. Yoshida Nutrient Solution (Yoshida et al.1976) served as control, whereas 0.5 mM boron (moderately toxic) and 1.5 mM boron (highly toxic). Boron excess (B) caused marked reduction in length, biomass and relative water content of the seedlings, with more reductions in B-sensitive cv. Malaviya-36 as compared with B-tolerant cv. Brown Gora. B-sensitive seedlings showed higher B uptake in roots and shoots compared to the tolerant. Scanning electron microscopy (SEM) revealed ultrastructural damage to the guard cells with excess boron. Energy dispersive X-ray analysis (EDXA) of rice leaves showed decline in concentration of P, S, Ca and Mg in seedlings on B treatment. Increased production of reactive oxygen species O2˙−, H2O2, lipid peroxides, alteration in activity of antioxidative enzymes and increased membrane permeability was observed in B treated seedlings compared to controls. Real time PCR analysis of stress regulatory genes indicated differential expression of SOD isoforms in the two sets of cultivars with B treatment. Interestingly seedlings of B-tolerant cultivar were characterized by higher level of expression of Fe-SOD and its further increased expression on B treatment. Results suggest that B toxicity involves ultrastructural and elemental changes, increased generation of ROS and altered antioxidative enzyme activities in rice seedlings and increased expression Fe-SOD isoform appears to be associated with B tolerance.