Transgenic hairy root lines from Scutellaria baicalensis overexpressing phenylalanine ammonia-lyase (PAL) (SbPAL1, SbPAL2, and SbAPL3) were established using an Agrobacterium rhizogenes-mediated transformation system. Stable genetic transformation with the SbPAL genes was confirmed by real-time PCR. These transgenic hairy root lines produced higher quantities flavones (i.e., baicalin, baicalein, and wogonin) than the control hairy root line. In particular, the wogonin content was increased by 4-11 times in the SbPAL1-, SbPAL2-, and SbPAL3-overexpressing hairy roots than the S. baicalensis wild-type roots. This research showed the importance of PAL in flavone biosynthesis and demonstrated the efficiency of metabolic engineering in S. baicalensis hairy roots. (C) 2012 Elsevier Ltd. All rights reserved.