Many types of nucleic acid, including canonical small interfering RNA (siRNA) duplexes, are potent activators of the mammalian innate immune system. Synthetic siRNA duplexes can induce high levels of inflammatory cytokines and type I interferons, in particular interferon-alpha, after systemic administration in mammals and in primary human blood cell cultures. These responses are greatly potentiated by the use of delivery vehicles that facilitate cellular uptake of the siRNA. Although the immunomodulatory effects of nucleic acids may be harnessed therapeutically, for example, in oncology and allergy applications, in many cases immune activation represents a significant undesirable side effect due to the toxicities associated with excessive cytokine release and associated inflammatory syndromes. The potential for siRNA-based drugs to be rendered immunogenic is also a cause for concern because the establishment of an antibody response may severely compromise both safety and efficacy. Clearly, there are significant implications both for the development of siRNA-based drugs and in the interpretation of gene-silencing effects elicited by siRNA. This review provides the background information required to anticipate, manage, and abrogate the immunological effects of siRNA and will assist the reader in the successful in vivo application of siRNA-based drugs.