The results of twin and family studies clearly implicate an important role for genetic factors in the etiology of systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). However, the complex nature of these diseases has hampered progress in defining the genetic determinants. Recent advances in molecular genetic and statistical methodology offer new hope to overcome these challenges. This review highlights recent efforts to identify genetic risk factors for SLE and RA using allele sharing and other linkage methods. In spite of striking differences between these studies, some agreement in terms of the regions providing evidence of linkage also exists. Thus, together these studies highlight regions of the genome that are likely to contain SLE and RA susceptibility genes. In addition, the results of these studies, in conjunction with progress in other complex human diseases, suggest several important considerations for future studies.