Boron (B) is an essential micronutrient for normal growth of higher plants. On the other hand, its toxicity is also a significant problem that can limit plant growth on soils of arid and semi-arid environments in agricultural regions across the world. In this study, two tomato (Lycopersicon esculentum Mill.) varieties (SC2121 and SAFARI F1) are used, and toxic effects of B treatment (3 mM) were studied. Germination was not affected, and seeds of both varieties germinated nearly to 100%. These in vitro germination experiments were accomplished in MS medium. Malondialdehyde (MDA) content, and antioxidant enzyme activites (superoxide dismutase (SOD), peroxidase (POX), catalase (CAT), ascorbate peroxidase (APX) and glutathione reductase (GR)) were investigated in root and shoot tissues of tomato seedlings.