Background : Cirsium plants have been used for perennial edible plants and grow wild in the mountainous regions of Korea, including Cirsium setidens and C. pendulum. In particular, C. setidens is commonly called 'gondre', and it has been used medicinally for diseases such as hematuria, hepatitis and hypertension. Hairy roots cultivation can be used as a method for increasing production through mass culture of medicinal plants, and elicitors such as methyl jasmonate (MeJa) can be treated to increase the content of certain useful ingredients. In this study, the hairy root was derived from the leaf tissues of C. setidens and C. pendulum, and the HPLC pattern was compared by MeJa treatment. Methods and Results : Agrobacterium rhizogenes R1000 was used to induce hairy roots in 1/2× MS medium. In addition, the hairy roots was treated with MeJa for different time (0, 1, 2, 5, 10, 24, 48, 72 h) and with various concentrations (0, 10, 50, 100, 200, 300 μM). The HPLC pattern changes were analyzed by on-line HPLC-ABTS. Four new peaks were observed in both Cirsium setidens and C. pendulum hairy roots, all of which showed antioxidant activity. In the case of C. pendulum, chlorogenic acid content was about 4 times higher than that of leaves. These peaks, including chlorogenic acid, were all affected by MeJa treatment. Conclusion : Four peaks were detected in the hairy roots of C. setidens and C. pendulum not in the leaves, and they were confirmed to be affected by the treatment of MeJa. It is necessary to clarify the structure through the subsequent compound separation.