Methanolic extracts of microshoots from agar cultures and of microshoots and media from agitated cultures of Scutellaria lateriflora grown on identical five variants of the Murashige-Skoog (MS) and Linsmaier-Skoog (LS) media with different 6-benzyladenine (BA) and 1-naphthaleneacetic acid (NAA) concentrations (0.5-3.0 mg/l) were analyzed for flavonoids (27 compounds), phenylpropanoid glycosides (2 compounds) and phenolic acids (19 compounds) using the DAD-HPLC method. The amounts of individual compounds and total amounts of the above mentioned metabolite groups in the biomass from both types of the tested cultures were dependent on the composition of basal media and concentrations of BA and NAA in the media variants. In media extracts, no metabolites were confirmed. Higher total amounts of flavonoids were obtained in agar cultures (max. 722.04 and 2989.55 mg/100 g DW on MS and LS media variants, respectively), which were 1.1 and 1.7 times higher, respectively, than in agitated cultures. In both types of cultures, glycosidic conjugates: baicalin and wogonoside were the main flavonoids (max. amounts: 513.93 and 1838.18 mg/100 g DW, and 305.92 and 700.85 mg/100 g DW in agar cultures on MS and LS variants, respectively). High amounts of verbascoside in agar cultures were also confirmed (max. 384.99 and 543.17 mg/100 g DW on MS and LS media variants, respectively). The cells grown in agitated cultures converted exogenous precursors, i.e. hydroquinone (HQ) and 4-hydroxybenzoic acid (4-HBAc) into arbutin (β-d-glucoside of HQ). The highest amount of this product reached 5.63 and 1.45 g/100 g DW after the addition of these two precursors, respectively. This is the first large-scale report documenting in vitro biosynthetic potential of Scutellaria lateriflora microshoots cultivated in two tested culture. Key message After testing of 10 media variants in two types of in vitro cultures high amounts of flavonoids (app. 3 g%) and verbascoside (0.54 g%) were obtained. Additionally, 5.6 g% of arbutin as hydroquinone β-d-glucosylation product was confirmed. Keywords American skullcap • In vitro culture • Scutellaria specific flavonoids • Verbascoside • Arbutin • HPLC analysis Abbreviations BA 6-Benzyladenine 3,4-DAc 3,4-Dihydroxyphenylacetic acid DAD-HPLC Diode-array detector-high performance liquid chromatography DW Dry weight FM Fresh biomass 4-HBAc 4-Hydroxybenzoic acid HQ Hydroquinone LS Linsmaier and Skoog MS Murashige and Skoog NAA 1-Naphthaleneacetic acid Communicated by Nokwanda Pearl Makunga.