Small interfering RNA (siRNAs), the main effector of RNA interference (RNAi), are now routinely used to assess gene function, both in vitro and in vivo, and many innovative screens have been reported on the use of RNAi to identify potential drug targets. Despite several technical advances, however, there are still many challenges in determining the ideal design of siRNA sequence, the activation of the immune system, off-target effects, and competition with endogenous microRNAs for cellular miRNA-processing machinery. Therefore, the translation of RNAi technology into the clinic depends on resolving these challenges. This chapter summarizes recent progress in siRNA design, sensing by the immune system, and discusses some of the promising approaches that are currently being explored in separating siRNA unwanted effects from gene silencing.