Systemic lupus erythematosus (SLE) is the prototype of complex autoimmune diseases and is characterized by extreme breakdown of self-tolerance which results in a wide range of immunologic abnormalities and immune complex formation. Genetic, hormonal and environmental factors are known to contribute to the expression of the disease. SLE is very heterogeneous in clinical manifestations and different autoantibodies may predict different set of clinical outcome, however, despite considerable accumulated knowledge, the detailed pathogenesis of SLE still remains unknown. In genetic studies, recent findings in gene expression analyses strongly support the direct role of cytokines and interferons in various immune dysregulations described in SLE. By recent advances in high-throughput SNP genotyping, the association studies of this complex disease have become more practical and for the first time new genetic association results can be confirmed in different population.