The purpose of this work is to develop methods for identifying high-affinity nucleic acid binding species from soluble mixtures of compounds. We have developed and applied an affinity chromatography method for identifying small molecules with high affinity for the telomerase RNA/DNA duplex. An affinity resin was derivatized with an RNA/DNA duplex which represents the key structure that forms during telomerase's catalytic cycle. A soluble mixture of compounds was applied to this resin and the compounds which bound to the highest extent were also confirmed to be the best inhibitors of the enzyme. This correlation of affinity for the RNA/DNA duplex with telomerase inhibition both supports the duplex as the target of these compounds, and suggests that the affinity method may be applied for the identification of higher affinity inhibitors from soluble mixtures of compounds.