Water and ethanol extracts of 67 species of medicinal plants were tested to determine antimicrobial activity against Helicobacter pylori. Among them, the extracts of Coptis japonica showed the best antibacterial activity. The extract of C. japonica showed four major spots on TLC plate and the Rf values of the spots were 0.07, 0.13, 0.21 and 0.73, respectively. Except for the spot of Rf 0.73, other three spots inhibited the cell growth of H. pylori. As shown in HPLC analysis, three antimicrobial spots contain berberine, major antimicrobial substance of C. japonica. However, the spot of Rf 0.13 had higher activity than berberine. The concentrated water extract of three prescribed medicines related with C. japonica showed good antibacterial activity against H. pylori.