The occurrence of autoimmunity is strongly associated with multiple gene variants that predispose individuals to disease. The identification of the gene polymorphisms that modulate disease susceptibility is key to our understanding of disease etiology and pathogenesis. While genetic studies in humans have uncovered several associations and have provided possible candidate genes for further study, the use of animal models is indispensable for detailed functional studies. In order to facilitate the genetic manipulation of experimental models of autoimmunity, we employ lentiviral transgenesis in combination with RNA interference (RNAi). This approach bypasses the need for targeted mutagenesis of embryonic stem cells and/or backcrossing of genetically modified animals onto the relevant genetic background. Lentiviral RNAi offers several advantages compared to conventional transgenesis or knockout technology, and these, as well as the technique’s weaknesses, are discussed herein.