Thioflavin T (ThT) is a commonly employed fluorescence probe for sensing amyloid fibrils. These highly ordered, insoluble nanostructures colocalize with sulfated glycosaminoglycans (GAGs) being abundant in the extracellular matrix and on the outer surface of cell membranes. To elucidate the positive impact of GAGs on amyloidogenesis, they are frequently used to promote fibril formation in vitro, which is detected by the enhanced fluorescence of ThT. The polyanionic nature and the affinity of GAGs to basic compounds predict that cationic ThT molecules may also bind to them, in addition to cross-β-structures formed in the reaction medium. By means of circular dichroism (CD) and absorption spectroscopy, this study examined the heparin and chondroitin sulfate binding of ThT. The large blue shift of the absorption peak indicated a card-pack type oligomerization of the dye molecules along the linear GAG chains. The strong exciton couplet observed in the CD spectra implies the left-handed, helical arrangement of GAG-associated oligomers of the dye. The decisive contribution of ionic forces for the binding was illustrated by sodium-ion-provoked dissociation of dye-GAG complexes. In silico analysis was performed to complement the experimental findings and to contribute to the understanding of potential molecular mechanisms underlying ThT-GAG interactions. ThT can be considered as an inert component in GAG-induced amyloid assays but only if the experiments are correctly designed.