The recent developments in genetic techniques and the development of more appropriate animal models for rheumatoid arthritis and multiple sclerosis make it possible to use a new approach for understanding these complex diseases. Thus it is now meaningful to address the question of which genes are causing the diseases. Several new associations with loci outside the MHC region have now been identified in models for both rheumatoid arthritis and multiple sclerosis. Some of these are shared between diseases - for example loci on mouse chromosome 3 (experimental allergic encephalomyelitis, collagen-induced arthritis and Theiler's encephalomyelitis) and rat chromosome 4 (collagen-induced arthritis and the experimental allergic encephalomyelitis induced by myelin oligodendrocytic glycoprotein).