ABC multidrug transporters are key players in cancer multidrug resistance and in determining the ADME-Tox properties of drugs and xenobiotics. The most sensitive and specific detection of these transporters is based on functional assays. Assessment of the transporter-dependent reduction of cellular uptake of the fluorescent dyes, such as Hoechst 33342 (Ho) and more recently DyeCycle Violet (DCV), have been widely advocated for the characterization of both ABCB1 and ABCG2 multidrug transporters. Detailed comparison of these supravital DNA-binding dyes revealed that DCV is less toxic to ABCG2-and ABCB1-expressing cells than Ho. ATPase measurements imply that DCV and Ho are similarly handled by ABCB1, whereas ABCG2 seems to transport DVC more effectively. In addition, we have developed an image-based high content microscopy screening method for simultaneous in situ measurement of the cellular activity and expression of the ABCG2 multidrug transporter. We demonstrated the applicability of this method for identifying ABCG2-positive cells in heterogeneous cell population by a single dye uptake measurement. These results may promote multidrug transporter studies at a single cell level and allow the quantitative detection of clinically important drug-resistant sub-populations. V C 2016 International Society for Advancement of Cytometry Key terms functional transporter assay; multidrug transporters; ABCG2; ABCB1; DyeCycle Violet; Hoechts 33342; high content screening and analysis MULTIDRUG resistance is a major problem in chemotherapy of cancer or in prolonged viral infections. An important cause of the emergence of cellular multidrug resistance is the increased expression of ABC multidrug transporters (1,2). Three human ABC proteins, ABCB1, ABCG2, and ABCC1 are the key membrane proteins responsible for an increased outward drug transport in most multidrug-resistant cells. These transporters are members of the ancient ABC transporter protein family, performing primary, ATP-dependent active transport processes. The human multidrug transporters consist of conserved cytoplasmic ABC domains, responsible for the ATP binding and hydrolysis, and multipass membrane region(s) involved in drug substrate binding and outward drug transport (3,4). The above mentioned three human multidrug transporters show promiscuous drug binding characteristics and have partially overlapping substrate specificities. Prediction of interactions between ABC multidrug transporters and drugs is a challenging task, because the structure of these proteins is not known at an atomic level, and the drug-protein interaction site is probably a large and versatile interface (5).Both in vitro and in vivo studies clearly indicate that in multidrug-resistant cells the therapeutically effective drug concentrations strongly depend on the actual, func-