In addition to "conventional" drug discovery targets used in modern strategies, mainly focusing on proteins, recent insights into gene regulation as a novel drug concept have begun to invite the targeting of biomolecular interactions between proteins and RNA. Because two protein-RNA interactions (Tat and trans-activation-responsive element, Rev and Rev-responsive element) are essential for any productive replication of human immunodeficiency virus, this important human pathogen was used as a model system for our studies. The design of a fluorescence-based high throughput assay, in which both targets were presented in the same vessel, enabled us to simultaneously interrogate two characteristics of a potential inhibitor: potency of interference and selectivity toward each of the interactions. Although related systems have been reported for several DNA binders, an extension into interference with transcription events would open a new dimension of cellular regulation. Here we describe the setup of the screening assay for over 110,000 compounds as well as a primary characterization of identified hits. The assay's characteristics demonstrate that a microwell-based dual screening system for RNA binders may add a powerful tool to modern drug discovery.