Heterogeneous sulfated polysaccharides have attracted significant attention in light of their various biological activities. However, recent events involving heparin have dramatically illustrated that several analytical challenges exist in accounting for such species. In this case, tainted heparin was associated with acute reactions that lead to numerous deaths. Researchers were forced to use time-consuming, sophisticated techniques (e.g., enzymatic digestion, NMR, CE, HPLC, MS, etc.) to identify the cause of these adverse effects. Extensive investigations ultimately showed oversulfated chondroitin sulfate, a semi-synthetic sulfated polysaccharide, to be present in the contaminated samples. These events highlighted the need for a new generation of screening techniques. In this work, we report the development of a screening strategy that exploits unique circular dichroism features observed as a function of association between investigated polymers and judiciously selected probe molecules (i.e., chloroquine, N1-(7-chloro-4-quinolinyl)-N3-methyl-1,3-propanediamine, quinacrine, and N2-9-acridinyl-N1,N1-dimethyl-1,2-ethanediamine). Application of obtained spectropolarimetry results to a flow injection analysis circular dichroism platform allowed for the establishment of linear polysaccharide response curves for dextran sulfate, heparin, and oversulfated chondroitin sulfate in the low micromolar range. Lastly, through additional work with heparin, the proposed method was shown to be capable of rapidly screening sulfated polysaccharide samples for closely related impurities.