Hammerhead ribozymes have been extensively used as RNA-inactivating agents for therapy as well as forward genomics. A ribozyme can be designed so as to specifically pair with virtually any target RNA, and cleave the phosphodiester backbone at a specified location, thereby functionally inactivating the RNA. Two major factors that determine whether ribozymes will be effective for posttranscriptional gene silencing are colocalization of the ribozyme and the target RNAs, and the choice of an appropriate target site on the mRNA. Complex secondary structures and the ability to bind to some of the cellular proteins mandate that some RNA sequences could stearically occlude binding of RNA-based antivirals like ribozymes to these sites. The use of ribozyme libraries in cell culture factors in these interactions to select for target sites on the RNA, which are more accessible to RNA-based antivirals like ribozymes or siRNA. This chapter provides a useful guide toward using ribozyme libraries to screen for effective target sites on mRNA.