Silybum marianum is an important medicinal plant with high antioxidant properties. Static magnetic field (SMF) is a kind of abiotic stresses which can affect growth and antioxidant capacity of medicinal plants. In this research, the effects of SMF on total phenolic and flavonoid contents, radical scavenging activity, and anatomical alterations were investigated in S. marianum seedlings. Five-day-old seedlings were treated with different intensities of SMF (0, 2, 4 and 6mT) for one hour, and then were irrigated with 1/2 Hoagland solution for four weeks. Results showed that SMF up to 4 mT increased fresh weight, dry weight, leaf area, relative water content (RWC), root length significantly and then decreased these parameters at 6 mT. At 4 mT, SMF caused an 125, 132. 73 and 52. 19% increase in dry weight, leaf area and root length as compared to the control, respectively. Metaxylem number and size, aerenchyma formation and stele diameter were improved under SMF. Lipid peroxidation (MDA) decreased especially at 4 mT, although H2O2 level increased in S. marianum shoots. Also, SMF induced total phenolic (93. 89%) and flavonoid contents (36. 43%), and decreased IC50 values (43. 01%) especially at 4 mT in leaves. The results suggest that SMF at proper frequency could improve antioxidant capacityof plant cells by regulation of H2O2 level and membrane stability.