A method of analysis of eight flavones using high-performance liquid chromatography (HPLC)-diode array detection (DAD)-mass spectrometry (MS) in root and aerial tissues of the medicinal plant Scutellaria baicalensis was developed. The identity of the analytes was confirmed using retention time, UV-vis and mass spectral comparisons to commercial standards. Both UV-vis and mass spectral patterns were characterized for glycosylated flavones. Two additional flavone glycosides were tentatively identified as chrysin-7-glucuronide and wogonoside, but not quantified. Greenhouse and in vitro-grown tissues were analyzed with flavone concentrations ranges of 0.14-150 and 0.030-1.7 microg/mg for greenhouse root and shoot tissue, respectively, and 0.0068-6.4 and 0.082-1.5 microg/mg for in vitro-grown roots and shoots, respectively.