At least 21 genes are encoded in the class II region of the human major histocompatibility complex on the short arm of chromosome six. Genes encoding the MHC-DR, DP and DQ molecules were identified first by virtue of their role in the immune response. DR, DP and DQ genes encode heterodimers expressed on the surface of B-cells. The surface class II molecules bind antigen and stimulate proliferation of T-cells directed against that antigen. In autoimmunity, the T-cell response is directed against a self-antigen. Since allelic variants of the DR, DP and DQ genes are associated with numerous autoimmune diseases, it has been proposed that these variants are particularly capable of presenting self-molecules. However, no autoimmune disease is always associated with any particular DR, DP or DQ variant. Large scale cloning of the class II region has revealed the presence of minor or unexpressed class II genes as well as genes not related to the "antigen presenting genes." It remains to be seen whether any of these recently identified genes explain the connection between the class II region and autoimmunity.