The inflammatory bowel diseases (IBD) and systemic lupus erythematosus (SLE) are common autoimmune diseases that affect 2-3 million people in the USA alone. Crohn's disease (CD) and ulcerative colitis (UC), the inflammatory bowel diseases, are idiopathic, chronic inflammatory disorders of the gastrointestinal tract. SLE is a chronic, multi-system autoimmune disease that generally presents in women of childbearing age as fatigue, arthralgia and rash. Although the aetiology of these two diseases is not fully known, it is believed that genetic, hormonal and environmental influences contribute to susceptibility. Genomewide linkage scans in IBD have revealed significant loci that, upon comprehensive association mapping strategies, yield what are believed to be causal susceptibility alleles. Human linkage studies performed to date in SLE have not been as informative, although genetic mapping in mouse models of SLE as well as candidate gene approaches have provided important clues to the genetic susceptibility in humans. We will examine how some of the recent advances in our understanding of genetic variation in the human genome are greatly improving our ability to map autoimmune disease genes in humans.