The immune system is comprised of biological structures and processes within an organism that protects against diseases. This system has been discussed extensively since the introduction of medicine and yet has remained the most enigmatic. Continuous research in the field has yielded better but not complete understanding of concepts of immunity and related disorders. Although researchers have learned much about the immune system, new technologies for identification of individual immune cells are now allowing scientists to determine which targets are triggering immune response against healthy self. The detailed understanding of immunological tolerance, its regulatory network, combination of new technologies and expanded genetic information may increase the awareness to make it possible to control degree of auto reactivity in the immune system and lay down new hope for treatment of autoimmune diseases in the future.