RNA silencing is an invaluable tool to interrogate gene function. The cytoplasmic delivery of small interfering RNAs (siRNAs) complementary to a gene of interest results in cleavage and degradation of the target mRNA. Given the potential to target virtually any RNA, siRNA-based therapeutics may revolutionize the treatment of disease. Target site accessibility is a significant barrier to the design and efficacy of siRNAs, particularly against highly structured targets such as the genomes of positive-sense RNA viruses. Here, we describe a bead-based approach to screen for target site accessibility of siRNAs designed against highly structured target RNAs and demonstrate that this approach can be used to assess target site accessibility in vitro and predict potent target sites for siRNAs in cell culture against a highly structured RNA target.