Cancer and autoimmunity are polygenic diseases. In order to better understand the mechanisms of disease development and progression it is essential to uncover which genes are involved. Much has been learned from population studies in human patients by searching for polymorphic genetic loci associated with disease. In addition, animal models of tumor development, as well as models for various autoimmune conditions such as multiple sclerosis and Type I diabetes, have helped determine genetic loci that contribute to disease susceptibility. However, characterization of the exact genes involved is often difficult and requires lengthy and technically demanding genetic manipulations. The generation of knockout animals is the method of choice to probe single genes. However, this is not possible in all species or even in all inbred strains within a species. The recent discovery of a new post-transcriptional gene silencing pathway termed RNA interference, which is mediated by short fragments of double-stranded RNA (short-interfering RNA), has opened up new avenues for genetic manipulation of experimental animals. This review will consider how silencing genes by RNA interference within the context of experimental disease models promises to become a powerful new tool for the genetic analysis of cancer and autoimmunity. Advances in RNA interference technology now permit the relatively rapid generation of transgenic animals in a wide range of species with complex genetic backgrounds that were previously inaccessible to genetic manipulation. This novel approach should help refine the characterization of disease-associated genes, either by silencing specific candidates or even by screening a larger number of genes in vivo within a comparatively short time frame.