Centaurea cyanus L. is a valuable source of many different bioactive substances. It is used in herbal medicine, but the structure of its organs used as raw material and secretory tissues has been insufficiently examined. The aim of this paper was to investigate the microstructure of C. cyanus flowers, bracts, stems and leaves with particular emphasis on secretory structures. Moreover, the main classes of secondary metabolites present in the secretion were identified and the taxonomic value of some micromorphological and anatomical features was analysed. Histochemical, micromorphological and ultrastructural analyses of aboveground organs of C. cyanus were carried out using light, fluorescence, scanning and transmission electron microscopy. The analyses revealed the presence of petal papillae and a characteristic cuticular pattern on the petals, stamens and stylar hairs. There were four types of non-glandular trichomes on the bracts, leaves and stem surfaces. The epidermal cells of the bracts contained prismatic calcium oxalate crystals. Two kinds of secretory structures, i.e. glandular trichomes and ducts, were observed in the C. cyanus organs. The glandular trichomes were located on the bract and stem surfaces, and the ducts were detected in the leaves and stems. Ultrastructural analyses of the epithelium of the ducts showed the presence of strongly osmiophilic insoluble phenolic material in vacuoles as well as moderately osmiophilic insoluble lipidic material in elaioplasts and vesicles. The results of histochemical assays showed a heterogeneous nature of the duct secretion, which contained essential oil, lipids, flavonoids, tannins and terpenes containing steroids