Thirty-three compounds were isolated from the root decoction of Isatis indigotica by using a combination of various chromatographic techniques including silica gel, macroporous adsorbent resin, Sephadex LH-20, and reversed-phase HPLC. Their structures were elucidated by spectroscopic data as (+)-dehydrovomifoliol (1), (S)-(+)-abscisic acid (2), vomifoliol (3), cyclo (L-Phe-L-Leu) (4), cyclo(L-Phe-L-Tyr) (5), cyclo(L-Tyr-L-Leu) (6), cyclo(L-Pro-L-Tyr) (7), evofolin B (8), (+)-syringaresinol (9), (-)-(7R,7'R,8S,8'S)-4,4'-dihydroxy-3-methoxy-7,9';7',9-diepoxy-lignan (10), (-)-medioresinol (11), (+) -(7R,7'R,8S,8'S) -neo-olivil (12), (-) -5-methoxyisolariciresinol (13), 1,3-dihydro-2H-indol-2-one (14), isalexin (15), dihydroneoascorbigen (16), indican (17), (-) -(S) -cyanomethyl-3-hydroxyoxindole (18), isoformononetein (19), calycosin (20), stigamast-5-ene-3beta-ol-7-one (21), acetovanillone (22), 3, 5-dimethoxy-4-hydroxyacetophenone (23), dihydroconiferyl alcohol (24), dihyroferulic acid (25), 3-hydroxy-1-(4-hydroxyphenyl) propan-1-one (26), beta-hydroxypropiovanillone (27), 4-aminobenzoic acid (28), 3-(4-hydroxyphenyl) propan-1-ol (29), 4-(2-hydroxyethyl) phenol (30), 2-methoxy-4-vinylphenol (31), pyrocatechol (32), and 4-pentenamide (33). These compounds were isolated from the root of I. indigotica for the first time. In preliminary in vitro assays, compound 19 showed activity against the influenza virus A/Hanfang/359/95 (H3N2), the herpes simplex virus 1 (HSV-1), and Coxsackie virus B3 (Cox-B3), with IC50 values of 2.06, 6.84, and 8.70 micromol x L(-1), respectively, but other compounds were in-active at a concentration of 1.0 x 10 x (-5) mol x L(-1).