The immune system has a number of mechanisms that are able to detect foreign pathogens by utilizing the major histocompatibility complex (MHC). This locus encodes the HLA genes and a variety of immune response (Ir) genes, thereby shaping the immune system that protects against pathogens. There are two main types of HLA antigens, HLA class I and class II. The function of HLA class I molecules is to present viral peptides at the surface of an infected cell to a T cell receptor (TCR) on a CD8 + T cell. The activation of these CD8 + T cells leads to the killing of the virally infected cell. This role of HLA class I, the identification of cells that are infected, explains why all nucleated cells have the capacity to express these MHC molecules. HLA class II molecules, in comparison, are expressed almost exclusively on the surface of dendritic cells, B lymphocytes, macrophages, endothelial cells, and activated T cells. Functionally, the HLA class II molecules present peptides to the TCR on CD4 + helper T cells. The engagement of the TCR by the peptide-MHC complex is necessary for the activation of CD4 + and CD8 + T cells, thereby leading to an effective adaptive immune response against an invading pathogen [15]. CD4 + T cells are central mediators of the adaptive immune response including cytokine secretion and cellular and humoral defenses against a pathogen. The HLA locus is extremely polymorphic leading to a heterogeneous population ensuring propagation of a species against novel pathogens. Unfortunately, this genetic heterogeneity adds to the complexity of identifying HLA genes implicated in autoimmune diseases.