The aims of the study were to evaluate the effect of media composition on the growth potential and morphology of the in vitro cultured biomass of three cultivars of Hypericum perforatum, and on the production of flavonoids. Agitated shoot cultures were maintained in parallel on Linsmaier and Skoog (LS) and Murashige and Skoog (MS) media supplemented with 0.1–3.0 mg L−1 of α-naphthaleneacetic acid and 6-benzylaminopurine. Methanolic extracts from the biomass collected after 3-wk growth cycles were analyzed quantitatively, for 21 flavonoids using high performance liquid chromatography. Three aglycones (kaempferol, luteolin, and quercetin) and three glycosides of quercetin (hyperoside, quercitrin, and rutoside) were detected in all of the extracts. The total amounts of the estimated compounds increased from 1.18- to 21.66-fold on LS media variants and from 1.52- to 17.34-fold on MS media variants. The main metabolite was quercetin (max. 210.55 mg 100 g−1 dry weight [DW]). The maximum total amounts of all compounds in the biomass of ‘Elixir,’ ‘Helos,’ and ‘Topas’ were 328.53, 255.70, and 166.58 mg 100 g−1 DW, respectively. The shoots of all cultivars cultivated on the LS and MS media containing low levels of plant growth regulators (0.1 mg L−1) accumulated high amounts of flavonoids. The highest amounts were accumulated in shoots of cultivar ‘Elixir’ grown on MS medium. This is the first comparison of flavonoid production in three cultivars of H. perforatum (‘Elixir,’ ‘Helos,’ and ‘Topas’) cultured in vitro, and the first report of flavonoid production in cultivars ‘Elixir’ and ‘Helos.’Electronic supplementary materialThe online version of this article (10.1007/s11627-018-9900-7) contains supplementary material, which is available to authorized users.