The active compounds in the roots of Scutellaria baicalensis Georgi, a traditional Chinese medicinal plant, are mainly flavonoids which have anti-inflammatory, antitumour, and anti-HIV activity, respectively. The increasing annual average temperature has rendered the S. baicalensis plants grown in some ancient producing regions no longer suitable for their medicinal usage. Hydrogen peroxide plays an important role in root responses to abnormal temperature in S. baicalensis. Baicalin and baicalein and antioxidative enzymes were anticipated to detoxify H2O2 in S. baicalensis. Here, we show that abnormal temperatures (10 and 40 degrees C) decreased the content of flavonoids as compared with the normal temperature (30 degrees C), and the transcripts of UDP-glucuronate:baicalein 7-O-glucuronosyltransferase and beta-glucuronidase involved in the interconversion between baicalin and baicalein were affected by the 40-degrees C treatment. High temperature also increased the activities of catalase and peroxidase. Reverse transcription-polymerase chain reaction (RT-PCR) analysis revealed that the transcript levels of peroxidase 2, peroxidase 3, monodehydroascorbate reductase 2, and dehydroascorbate reductase were significantly increased under high-temperature conditions. The respective genes would be candidates for improvement of the adaptation of S. baicalensis plants to abnormal temperatures and for regulation of the contents of the active compounds.