Secretory ducts and cavities of roots and rhizomes are typical features of the Cardueae tribe in the Asteraceae family. We used light microscopy to analyze the anatomy of the subterranean organs of 21 species of 13 genera of the Cardueae, with particular attention to the secretory system, interpreted in taxonomic terms. The anatomy of secretory ducts varied greatly. A new measurement quotient, C1 [length of epithelial cells (longitudinal section)] and C2 [length of adjacent cells (longitudinal section)] was established. Different types of ducts are described based on type of development and the size ratios among epithelial cells. Detailed anatomical descriptions of the ducts are given, together with their occurrence in particular taxa. The simultaneous presence of various secretory ducts within a single species and their spatial position relative to other prominent anatomical features provide valuable characters for discriminating the studied Cardueae species. These analyses are of particular interest for identification of herbal drugs as, besides chemical analytical techniques such as chromatographic fingerprinting, light microscopy is a common method for purity controls and thus required in official pharmacopeias.