Autoimmunity cannot yet be prevented or cured, in large part due to our poor understanding of disease etiology. Remarkable advances in genomic technology have recently enabled the discovery of a large number of disease-associated gene variations by genome-wide association studies. The next step towards understanding autoimmune disorders entails the functional study of susceptibility genes within experimental disease models. RNA interference (RNAi) is a promising tool for such investigations. Several features of RNAi, including its specificity, versatility and reversible nature, allow experimental systems to be tailored to relevant gene variations. This review discusses how the experimental use of RNAi is invaluable in bridging the gap between the identification of susceptibility genes and the elucidation of their functional contribution to autoimmune disease.