Autoimmune diseases are estimated to affect 10–50 million people in the United States, and untold millions worldwide. Nearly 80% of all people with autoimmune diseases are women, and a strong association of these diseases with MHC genes has been known for some time. However, very little is known about what causes autoimmune diseases or the factors that lead to disease recurrence. The sex-associated differences in multiple sclerosis (MS) and the mouse model of MS, experimental autoimmune encephalomyelitis (EAE), are associated with MHC genetic background, sex hormone levels and cytokine production. The implication of these factors has aided the identification of new autosomal genetic susceptibility loci. Complete deficiencies of early complement components are strongly associated with systemic lupus erythematosus (SLE) but the role of complement proteins in SLE is not yet clear. Recent data suggest that quantitative and qualitative diversities of the MHC-linked complement C4 among different ethnic groups can be important in the susceptibility and disease severity of SLE.