“Ribozymes” are RNA molecules with enzymatic properties [1]. These are naturally occurring moieties that provide fine-tuning of the gene expression cascades (replication, transcription and translation) by catalyzing essential steps such as cleavage and ligation [2]. Hammerhead ribozymes (for resemblance of their two-dimensional structure to a hammerhead) are the smallest ribozymes that are used as molecular scissors in molecular biology and biotechnology to elucidate and eliminate gene functions. The RNA is induced to fold into its active conformation by the binding of metal ions. It forms two domains; the scaffold (“domain 2”) on which the ribozyme is built and the active centre (catalytic domain called “domain I”) of the ribozyme [3, 4]. Over the last two decades, mechanism of action of hammerhead ribozymes describing the requirement of divalent metal ion, definition of the catalytic domains and sequence specificity usually referred to as target site have been largely demonstrated [4–6]. Ribozyme activity in vivo critically depends on its effective level of expression, specificity, intracellular stability, target colocalization and accessibility to the target sites [7]. These technical issues imposed a major difficulty in the use of ribozymes in vivo. Various modifications of the ribozyme expression plasmid have subsequently thus come into play. For example, it was shown that the ribozymes expressed under the control of RNA polymerase III promoter (tRNAVal promoter) were efficiently expressed, highly stable and were exported to the cytoplasm [7]. Such expression improved the ribozyme activity in vivo by many folds. However, efficiently expressed and highly stable ribozymes may still lack action due to their inaccessibility to the target sites that in turn imposed a major hurdle because of the unforeseeable secondary and tertiary RNA structures. Recently, this obstacle was elegantly resolved by modifying the ribozyme expression plasmids. A novel hybrid ribozyme that combined the cleavage activity of hammerhead ribozyme with the unwinding activity of the endogenous RNA helicase was developed. Such RNA helicase based hybrid ribozymes expressed from RNA polymerase III promoter (tRNAVal) were indeed shown to have substrate-unwinding as well as strong cleavage activity [8, 9]. Such hybrid ribozymes can attack most, if not all, sites within mRNA. Thus, it was possible to prepare libraries of hybrid ribozymes with randomized binding arms and to examine their effects after they have been introduced into cells. This novel system has many potential applications such as, elucidation of molecular mechanism of biological phenotypes including aging and cancer by identification of novel genes and their intervention by gene targeting. This chapter is dedicated to the molecularand technical details on the use of hammerhead ribozymes and their improved versions for identification of novel functional genes and their role in biological phenotypes.